7u2j - Revision history

OCA at 11:16, 15 November 2023

OCA — Wed, 15 Nov 2023 11:16:52 GMT

←Older revision		Revision as of 11:16, 15 November 2023
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	</div>		</div>
	<div class="pdbe-citations 7u2j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7u2j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribosomal protein THX 3D structures\|Ribosomal protein THX 3D structures]]
		+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:10, 18 October 2023

OCA — Wed, 18 Oct 2023 17:10:38 GMT

←Older revision		Revision as of 17:10, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7u2j]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7U2J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U2J FirstGlance]. <br>		<table><tr><td colspan='2'>[[7u2j]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7U2J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U2J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=8AN:3-AMINO-3-DEOXYADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>8AN</scene>, <scene name='pdbligand=CLM:CHLORAMPHENICOL'>CLM</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=L3X:3-deoxy-3-(glycylamino)adenosine+5-(dihydrogen+phosphate)'>L3X</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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]] 2.55Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=8AN:3-AMINO-3-DEOXYADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>8AN</scene>, <scene name='pdbligand=CLM:CHLORAMPHENICOL'>CLM</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=L3X:3-deoxy-3-(glycylamino)adenosine+5-(dihydrogen+phosphate)'>L3X</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=7u2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u2j OCA], [https://pdbe.org/7u2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u2j RCSB], [https://www.ebi.ac.uk/pdbsum/7u2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u2j 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=7u2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u2j OCA], [https://pdbe.org/7u2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u2j RCSB], [https://www.ebi.ac.uk/pdbsum/7u2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u2j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RL2_THET8 RL2_THET8]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_B]	+	[https://www.uniprot.org/uniprot/RL2_THET8 RL2_THET8] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_B]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 03:55, 8 September 2022

OCA — Thu, 08 Sep 2022 03:55:06 GMT

←Older revision		Revision as of 03:55, 8 September 2022
Line 1:		Line 1:

-	====	+	==Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, peptidyl P-site fMAC-NH-tRNAmet, deacylated E-site tRNAgly, and chloramphenicol at 2.55A resolution==
-	<StructureSection load='7u2j' size='340' side='right'caption='[[7u2j]]' scene=''>	+	<StructureSection load='7u2j' size='340' side='right'caption='[[7u2j]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7u2j]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7U2J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U2J FirstGlance]. <br>
-	</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=7u2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u2j OCA], [https://pdbe.org/7u2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u2j RCSB], [https://www.ebi.ac.uk/pdbsum/7u2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u2j ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0TD:(3S)-3-(METHYLSULFANYL)-L-ASPARTIC+ACID'>0TD</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4OC:4N,O2-METHYLCYTIDINE-5-MONOPHOSPHATE'>4OC</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=8AN:3-AMINO-3-DEOXYADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>8AN</scene>, <scene name='pdbligand=CLM:CHLORAMPHENICOL'>CLM</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=L3X:3-deoxy-3-(glycylamino)adenosine+5-(dihydrogen+phosphate)'>L3X</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=7u2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u2j OCA], [https://pdbe.org/7u2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u2j RCSB], [https://www.ebi.ac.uk/pdbsum/7u2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u2j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/RL2_THET8 RL2_THET8]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_B]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosome serves as a universal molecular machine capable of synthesis of all the proteins in a cell. Small-molecule inhibitors, such as ribosome-targeting antibiotics, can compromise the catalytic versatility of the ribosome in a context-dependent fashion, preventing transpeptidation only between particular combinations of substrates. Classic peptidyl transferase center inhibitor chloramphenicol (CHL) fails to inhibit transpeptidation reaction when the incoming A site acceptor substrate is glycine, and the molecular basis for this phenomenon is unknown. Here, we present a set of high-resolution X-ray crystal structures that explain why CHL is unable to inhibit peptide bond formation between the incoming glycyl-tRNA and a nascent peptide that otherwise is conducive to the drug action. Our structures reveal that fully accommodated glycine residue can co-exist in the A site with the ribosome-bound CHL. Moreover, binding of CHL to a ribosome complex carrying glycyl-tRNA does not affect the positions of the reacting substrates, leaving the peptide bond formation reaction unperturbed. These data exemplify how small-molecule inhibitors can reshape the A-site amino acid binding pocket rendering it permissive only for specific amino acid residues and rejective for the other substrates extending our detailed understanding of the modes of action of ribosomal antibiotics.
		+
		+	Structural basis for the inability of chloramphenicol to inhibit peptide bond formation in the presence of A-site glycine.,Syroegin EA, Aleksandrova EV, Polikanov YS Nucleic Acids Res. 2022 Jul 22;50(13):7669-7679. doi: 10.1093/nar/gkac548. PMID:35766409<ref>PMID:35766409</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7u2j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Thermus thermophilus HB8]]
		+	[[Category: Aleksandrova EV]]
		+	[[Category: Polikanov YS]]
		+	[[Category: Syroegin EA]]

OCA at 05:17, 13 July 2022

OCA — Wed, 13 Jul 2022 05:17:48 GMT

←Older revision		Revision as of 05:17, 13 July 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7u2j ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7u2j' size='340' side='right'caption='[[7u2j]]' scene=''>
-	~~Authors~~: ~~Syroegin, E~~.A.~~, Aleksandrova, E~~.V.~~, Polikanov, Y~~.S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA~~, ~~aminoacylated A~~-~~site Gly-NH-tRNAgly~~, ~~peptidyl P-site fMAC-NH-tRNAmet, deacylated E-site tRNAgly, and chloramphenicol at 2~~.~~55A resolution~~	+	</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=7u2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u2j OCA], [https://pdbe.org/7u2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u2j RCSB], [https://www.ebi.ac.uk/pdbsum/7u2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u2j ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures]~~]	+	</table>
-	[~~[Category~~: ~~Polikanov, Y~~.S]]	+	__TOC__
-	[[Category: ~~Syroegin, E.A~~]]	+	</StructureSection>
-	[[Category: ~~Aleksandrova, E.V~~]]	+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA: Protected "7u2j" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2022 05:09:14 GMT

Protected "7u2j" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:09, 2 March 2022

OCA: New page: '''Unreleased structure''' The entry 7u2j is ON HOLD Authors: Syroegin, E.A., Aleksandrova, E.V., Polikanov, Y.S. Description: Crystal structure of the Thermus thermophilus 70S ribosom...

OCA — Wed, 02 Mar 2022 05:09:13 GMT

New page: '''Unreleased structure''' The entry 7u2j is ON HOLD Authors: Syroegin, E.A., Aleksandrova, E.V., Polikanov, Y.S. Description: Crystal structure of the Thermus thermophilus 70S ribosom...

New page

'''Unreleased structure'''

The entry 7u2j is ON HOLD

Authors: Syroegin, E.A., Aleksandrova, E.V., Polikanov, Y.S.

Description: Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Gly-NH-tRNAgly, peptidyl P-site fMAC-NH-tRNAmet, deacylated E-site tRNAgly, and chloramphenicol at 2.55A resolution
[[Category: Unreleased Structures]]
[[Category: Polikanov, Y.S]]
[[Category: Syroegin, E.A]]
[[Category: Aleksandrova, E.V]]