4aqy - Revision history

OCA at 11:33, 20 December 2023

OCA — Wed, 20 Dec 2023 11:33:25 GMT

←Older revision		Revision as of 11:33, 20 December 2023
Line 3:		Line 3:
	<StructureSection load='4aqy' size='340' side='right'caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4aqy' size='340' side='right'caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4aqy]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AQY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.5Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [https://pdbe.org/4aqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [https://www.ebi.ac.uk/pdbsum/4aqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4aqy ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [https://pdbe.org/4aqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [https://www.ebi.ac.uk/pdbsum/4aqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4aqy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~RSHX_THETH RSHX_THETH~~]~~] Binds at the top of~~ the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-~~end of the 16S rRNA where it nucleates assembly of the head domain~~ of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[https://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[https://www.uniprot.org/uniprot/RS16_THETH RS16_THETH]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. [[https://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[https://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] Interacts with ~~and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of~~ the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] [[https://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[https://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[https://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[https://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[https://www.uniprot.org/uniprot/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[https://www.uniprot.org/uniprot/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[https://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:~~MF_01307_B~~]	+	[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Akbergenov, R]]	+	[[Category: Akbergenov R]]
-	[[Category: Bottger~~, E C~~]]	+	[[Category: Bottger EC]]
-	[[Category: Dubbaka~~, S R~~]]	+	[[Category: Dubbaka SR]]
-	[[Category: Duscha, S]]	+	[[Category: Duscha S]]
-	[[Category: Lang, K]]	+	[[Category: Lang K]]
-	[[Category: Matt, T]]	+	[[Category: Matt T]]
-	[[Category: Meyer, M]]	+	[[Category: Meyer M]]
-	[[Category: Ng~~, C L~~]]	+	[[Category: Ng CL]]
-	[[Category: Perez-Fernandez, D]]	+	[[Category: Perez-Fernandez D]]
-	[[Category: Ramakrishnan, V]]	+	[[Category: Ramakrishnan V]]
-	[[Category: Schacht, J]]	+	[[Category: Schacht J]]
-	[[Category: Sha~~, S H~~]]	+	[[Category: Sha SH]]
-	[[Category: Shcherbakov, D]]	+	[[Category: Shcherbakov D]]
-	[[Category: Vasella, A]]	+	[[Category: Vasella A]]
-	[[Category: Xie, J]]	+	[[Category: Xie J]]
-	~~[[Category: Apramycin]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Toxicity~~]]	+

OCA at 05:43, 25 August 2022

OCA — Thu, 25 Aug 2022 05:43:21 GMT

←Older revision		Revision as of 05:43, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='4aqy' size='340' side='right'caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4aqy' size='340' side='right'caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4AQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AQY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</div></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [~~http~~://pdbe.org/4aqy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4aqy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4aqy ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [https://pdbe.org/4aqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [https://www.ebi.ac.uk/pdbsum/4aqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4aqy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[~~http~~://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[~~http~~://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[~~http~~://www.uniprot.org/uniprot/RS16_THETH RS16_THETH]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. [[~~http~~://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[~~http~~://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] [[~~http~~://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[~~http~~://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[~~http~~://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[~~http~~://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[~~http~~://www.uniprot.org/uniprot/~~RS19_THETH RS19_THETH~~]] ~~Protein S19 forms a complex with S13 that binds strongly~~ to the ~~16S ribosomal RNA~~ (By similarity). [[~~http~~://www.uniprot.org/uniprot/~~RS10_THETH RS10_THETH~~]] ~~Involved in the binding of tRNA~~ to the ~~ribosomes~~ (By similarity). [[~~http~~://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B]	+	[[https://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[https://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[https://www.uniprot.org/uniprot/RS16_THETH RS16_THETH]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. [[https://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[https://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] [[https://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[https://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[https://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[https://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[https://www.uniprot.org/uniprot/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[https://www.uniprot.org/uniprot/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[https://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
		+	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
	*[[Ribosome 3D structures\|Ribosome 3D structures]]		*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==

OCA at 07:18, 23 May 2019

OCA — Thu, 23 May 2019 07:18:40 GMT

←Older revision		Revision as of 07:18, 23 May 2019
Line 1:		Line 1:

	==Structure of ribosome-apramycin complexes==		==Structure of ribosome-apramycin complexes==
-	<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='4aqy' size='340' side='right'caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>
Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Akbergenov, R]]		[[Category: Akbergenov, R]]

OCA at 08:03, 6 March 2019

OCA — Wed, 06 Mar 2019 08:03:32 GMT

←Older revision		Revision as of 08:03, 6 March 2019
Line 1:		Line 1:

	==Structure of ribosome-apramycin complexes==		==Structure of ribosome-apramycin complexes==
-	<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>		<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>

OCA at 09:04, 30 January 2019

OCA — Wed, 30 Jan 2019 09:04:24 GMT

←Older revision		Revision as of 09:04, 30 January 2019
Line 9:		Line 9:
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS16_THETH RS16_THETH]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. [[http://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/~~RS10_THETH RS10_THETH~~]] ~~Involved in the binding of tRNA~~ to the ~~ribosomes~~ (By similarity). [[http://www.uniprot.org/uniprot/~~RS19_THETH RS19_THETH~~]] ~~Protein S19 forms a complex with S13 that binds strongly~~ to the ~~16S ribosomal RNA~~ (By similarity). [[http://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B]	+	[[http://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS16_THETH RS16_THETH]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. [[http://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 11:52, 5 August 2016

OCA — Fri, 05 Aug 2016 11:52:52 GMT

←Older revision		Revision as of 11:52, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of ribosome-apramycin complexes==		==Structure of ribosome-apramycin complexes==
	<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [http://www.ebi.ac.uk/pdbsum/4aqy PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [http://pdbe.org/4aqy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [http://www.ebi.ac.uk/pdbsum/4aqy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4aqy ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4aqy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 02:13, 25 December 2014

OCA — Thu, 25 Dec 2014 02:13:06 GMT

←Older revision		Revision as of 02:13, 25 December 2014
Line 7:		Line 7:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [http://www.ebi.ac.uk/pdbsum/4aqy PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [http://www.ebi.ac.uk/pdbsum/4aqy PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RSHX_THETH RSHX_THETH]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS17_THETH RS17_THETH]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS16_THETH RS16_THETH]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains. [[http://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B] Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit (By similarity).[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). [[http://www.uniprot.org/uniprot/RS15_THETH RS15_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[http://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B] Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity).[HAMAP-Rule:MF_01307_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:

	==See Also==		==See Also==
-	*[[Ribosomal protein THX\|Ribosomal protein THX]]
	*[[Ribosome 3D structures\|Ribosome 3D structures]]		*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==
Line 24:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Akbergenov, R.]]	+	[[Category: Akbergenov, R]]
-	[[Category: Bottger, E C.]]	+	[[Category: Bottger, E C]]
-	[[Category: Dubbaka, S R.]]	+	[[Category: Dubbaka, S R]]
-	[[Category: Duscha, S.]]	+	[[Category: Duscha, S]]
-	[[Category: Lang, K.]]	+	[[Category: Lang, K]]
-	[[Category: Matt, T.]]	+	[[Category: Matt, T]]
-	[[Category: Meyer, M.]]	+	[[Category: Meyer, M]]
-	[[Category: Ng, C L.]]	+	[[Category: Ng, C L]]
-	[[Category: Perez-Fernandez, D.]]	+	[[Category: Perez-Fernandez, D]]
-	[[Category: Ramakrishnan, V.]]	+	[[Category: Ramakrishnan, V]]
-	[[Category: Schacht, J.]]	+	[[Category: Schacht, J]]
-	[[Category: Sha, S H.]]	+	[[Category: Sha, S H]]
-	[[Category: Shcherbakov, D.]]	+	[[Category: Shcherbakov, D]]
-	[[Category: Vasella, A.]]	+	[[Category: Vasella, A]]
-	[[Category: Xie, J.]]	+	[[Category: Xie, J]]
	[[Category: Apramycin]]		[[Category: Apramycin]]
	[[Category: Ribosome]]		[[Category: Ribosome]]
	[[Category: Toxicity]]		[[Category: Toxicity]]

OCA at 15:17, 12 October 2014

OCA — Sun, 12 Oct 2014 15:17:10 GMT

←Older revision		Revision as of 15:17, 12 October 2014
Line 2:		Line 2:
	<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from ~~[http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and~~ [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</td></tr>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Akbergenov, R.]]		[[Category: Akbergenov, R.]]

OCA at 05:40, 8 October 2014

OCA — Wed, 08 Oct 2014 05:40:20 GMT

←Older revision		Revision as of 05:40, 8 October 2014
Line 1:		Line 1:
-	==Structure of ~~ribsome~~-apramycin complexes==	+	==Structure of ribosome-apramycin complexes==
	<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [http://www.ebi.ac.uk/pdbsum/4aqy PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [http://www.ebi.ac.uk/pdbsum/4aqy PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 13:
	Dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin.,Matt T, Ng CL, Lang K, Sha SH, Akbergenov R, Shcherbakov D, Meyer M, Duscha S, Xie J, Dubbaka SR, Perez-Fernandez D, Vasella A, Ramakrishnan V, Schacht J, Bottger EC Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10984-9. Epub 2012 Jun 14. PMID:22699498<ref>PMID:22699498</ref>		Dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin.,Matt T, Ng CL, Lang K, Sha SH, Akbergenov R, Shcherbakov D, Meyer M, Duscha S, Xie J, Dubbaka SR, Perez-Fernandez D, Vasella A, Ramakrishnan V, Schacht J, Bottger EC Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10984-9. Epub 2012 Jun 14. PMID:22699498<ref>PMID:22699498</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>

Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Akbergenov, R.]]		[[Category: Akbergenov, R.]]

OCA at 07:18, 5 June 2014

OCA — Thu, 05 Jun 2014 07:18:38 GMT

←Older revision		Revision as of 07:18, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~4aqy.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Structure of ribsome-apramycin complexes==
		+	<StructureSection load='4aqy' size='340' side='right' caption='[[4aqy]], [[Resolution\|resolution]] 3.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4aqy]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AQY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AM2:APRAMYCIN'>AM2</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ab3\|1ab3]], [[1an7\|1an7]], [[1cqm\|1cqm]], [[1cqn\|1cqn]], [[1dv4\|1dv4]], [[1eg0\|1eg0]], [[1emw\|1emw]], [[1fjg\|1fjg]], [[1fka\|1fka]], [[1gix\|1gix]], [[1hnw\|1hnw]], [[1hnx\|1hnx]], [[1hnz\|1hnz]], [[1hr0\|1hr0]], [[1i94\|1i94]], [[1i95\|1i95]], [[1i96\|1i96]], [[1i97\|1i97]], [[1ibk\|1ibk]], [[1ibl\|1ibl]], [[1ibm\|1ibm]], [[1j5e\|1j5e]], [[1jgo\|1jgo]], [[1jgp\|1jgp]], [[1jgq\|1jgq]], [[1kuq\|1kuq]], [[1l1u\|1l1u]], [[1lou\|1lou]], [[1mvr\|1mvr]], [[1n32\|1n32]], [[1n33\|1n33]], [[1n34\|1n34]], [[1n36\|1n36]], [[1pns\|1pns]], [[1pnx\|1pnx]], [[1qd7\|1qd7]], [[1qjh\|1qjh]], [[1qkf\|1qkf]], [[1qkh\|1qkh]], [[1ris\|1ris]], [[1rss\|1rss]], [[1twt\|1twt]], [[1vox\|1vox]], [[1voz\|1voz]], [[1xmo\|1xmo]], [[1xmq\|1xmq]], [[1xnq\|1xnq]], [[1xnr\|1xnr]], [[1yl4\|1yl4]], [[2b64\|2b64]], [[2b9m\|2b9m]], [[2b9o\|2b9o]], [[2bvz\|2bvz]], [[2bxj\|2bxj]], [[2f4v\|2f4v]], [[2j00\|2j00]], [[2j02\|2j02]], [[2jl7\|2jl7]], [[2uu9\|2uu9]], [[2uua\|2uua]], [[2uub\|2uub]], [[2uuc\|2uuc]], [[2uxb\|2uxb]], [[2uxc\|2uxc]], [[2uxd\|2uxd]], [[2v46\|2v46]], [[2v48\|2v48]], [[2vqe\|2vqe]], [[2vqf\|2vqf]], [[2wdg\|2wdg]], [[2wdh\|2wdh]], [[2wdk\|2wdk]], [[2wdm\|2wdm]], [[2wh1\|2wh1]], [[2wh3\|2wh3]], [[2wrn\|2wrn]], [[2wrq\|2wrq]], [[2x9r\|2x9r]], [[2x9t\|2x9t]], [[2xfz\|2xfz]], [[2xg1\|2xg1]], [[2xqd\|2xqd]], [[2xsy\|2xsy]], [[2xuy\|2xuy]], [[2y0u\|2y0u]], [[2y0w\|2y0w]], [[2y0y\|2y0y]], [[2y10\|2y10]], [[2y12\|2y12]], [[2y14\|2y14]], [[2y18\|2y18]], [[3zvo\|3zvo]], [[4abr\|4abr]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4aqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4aqy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4aqy RCSB], [http://www.ebi.ac.uk/pdbsum/4aqy PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aminoglycosides are potent antibacterials, but therapy is compromised by substantial toxicity causing, in particular, irreversible hearing loss. Aminoglycoside ototoxicity occurs both in a sporadic dose-dependent and in a genetically predisposed fashion. We recently have developed a mechanistic concept that postulates a key role for the mitochondrial ribosome (mitoribosome) in aminoglycoside ototoxicity. We now report on the surprising finding that apramycin, a structurally unique aminoglycoside licensed for veterinary use, shows little activity toward eukaryotic ribosomes, including hybrid ribosomes which were genetically engineered to carry the mitoribosomal aminoglycoside-susceptibility A1555G allele. In ex vivo cultures of cochlear explants and in the in vivo guinea pig model of chronic ototoxicity, apramycin causes only little hair cell damage and hearing loss but it is a potent antibacterial with good activity against a range of clinical pathogens, including multidrug-resistant Mycobacterium tuberculosis. These data provide proof of concept that antibacterial activity can be dissected from aminoglycoside ototoxicity. Together with 3D structures of apramycin-ribosome complexes at 3.5-A resolution, our results provide a conceptual framework for further development of less toxic aminoglycosides by hypothesis-driven chemical synthesis.

-	~~{{STRUCTURE_4aqy\| PDB=4aqy \| SCENE= }}~~	+	Dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin.,Matt T, Ng CL, Lang K, Sha SH, Akbergenov R, Shcherbakov D, Meyer M, Duscha S, Xie J, Dubbaka SR, Perez-Fernandez D, Vasella A, Ramakrishnan V, Schacht J, Bottger EC Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10984-9. Epub 2012 Jun 14. PMID:22699498<ref>PMID:22699498</ref>

-	~~===Structure~~ of ~~ribsome-apramycin complexes===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_22699498}}~~	+	==See Also==
-		+	*[[Ribosomal protein THX\|Ribosomal protein THX]]
-	==~~About this Structure~~==	+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
-	[[~~4aqy~~]] ~~is a 23 chain structure with sequence from~~ [~~http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AQY OCA~~].	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	<~~ref group="xtra">PMID:022699498<~~/~~ref~~><~~references group="xtra"~~/>	+	</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Akbergenov, R.]]		[[Category: Akbergenov, R.]]