1bxe - Revision history

OCA at 15:36, 13 March 2024

2024-03-13T15:36:53Z

←Older revision		Revision as of 15:36, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1bxe' size='340' side='right'caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1bxe' size='340' side='right'caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BXE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bxe]] is a 1 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=1BXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BXE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.9Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [https://pdbe.org/1bxe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [https://www.ebi.ac.uk/pdbsum/1bxe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bxe 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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [https://pdbe.org/1bxe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [https://www.ebi.ac.uk/pdbsum/1bxe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bxe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RL22_THETH RL22_THETH]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome. This extension seems to form part of the wall of the exit tunnel (By similarity). Deleting residues 82 to 84 (the equivalent deletion in E.coli renders cells resistant to erythromycin) would probably cause the tip of the hairpin to penetrate into the tunnel.	+	[https://www.uniprot.org/uniprot/RL22_THETH RL22_THETH] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome. This extension seems to form part of the wall of the exit tunnel (By similarity). Deleting residues 82 to 84 (the equivalent deletion in E.coli renders cells resistant to erythromycin) would probably cause the tip of the hairpin to penetrate into the tunnel.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bxe ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bxe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Background:. The ribosomal protein L22 is one of five proteins necessary for the formation of an early folding intermediate of the 23S rRNA. L22 has been found on the cytoplasmic side of the 50S ribosomal subunit. It can also be labeled by an erythromycin derivative bound close to the peptidyl-transfer center at the interface side of the 50S subunit, and the amino acid sequence of an erythromycin-resistant mutant is known. Knowing the structure of the protein may resolve this apparent conflict regarding the location of L22 on the ribosome. Results:. The structure of Thermus thermophilus L22 was solved using X-ray crystallography. L22 consists of a small alpha+beta domain and a protruding beta hairpin that is 30 A long. A large part of the surface area of the protein has the potential to be involved in interactions with rRNA. A structural similarity to other RNA-binding proteins is found, possibly indicating a common evolutionary origin. Conclusions:. The extensive surface area of L22 has the characteristics of an RNA-binding protein, consistent with its role in the folding of the 23S rRNA. The erythromycin-resistance conferring mutation is located in the protruding beta hairpin that is postulated to be important in L22-rRNA interactions. This region of the protein might be at the erythromycin-binding site close to the peptidyl transferase center, whereas the opposite end may be exposed to the cytoplasm.
-
-	The crystal structure of ribosomal protein L22 from Thermus thermophilus: insights into the mechanism of erythromycin resistance.,Unge J, berg A, Al-Kharadaghi S, Nikulin A, Nikonov S, Davydova N, Nevskaya N, Garber M, Liljas A Structure. 1998 Dec 15;6(12):1577-86. PMID:9862810<ref>PMID:9862810</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1bxe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribosomal protein L22\|Ribosomal protein L22]]		*[[Ribosomal protein L22\|Ribosomal protein L22]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Aberg, A]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Al-Karadaghi, S]]	+	[[Category: Aberg A]]
-	[[Category: Davydova, N]]	+	[[Category: Al-Karadaghi S]]
-	[[Category: Garber, M]]	+	[[Category: Davydova N]]
-	[[Category: Liljas, A]]	+	[[Category: Garber M]]
-	[[Category: Nevskaya, N]]	+	[[Category: Liljas A]]
-	[[Category: Nikonov, S]]	+	[[Category: Nevskaya N]]
-	[[Category: Nikulin, A]]	+	[[Category: Nikonov S]]
-	[[Category: Unge, J]]	+	[[Category: Nikulin A]]
-	~~[[Category: Antibiotics resistance]]~~	+	[[Category: Unge J]]
-	~~[[Category: Protein synthesis]]~~	+
-	~~[[Category: Ribosomal protein]]~~	+
-	~~[[Category: Rna binding]]~~	+
-	~~[[Category: Rna binding protein~~]]	+

OCA at 07:13, 22 September 2021

2021-09-22T07:13:47Z

←Older revision		Revision as of 07:13, 22 September 2021
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	<StructureSection load='1bxe' size='340' side='right'caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1bxe' size='340' side='right'caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BXE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BXE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [~~http~~://pdbe.org/1bxe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1bxe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bxe 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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [https://pdbe.org/1bxe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [https://www.ebi.ac.uk/pdbsum/1bxe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bxe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RL22_THETH RL22_THETH]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome. This extension seems to form part of the wall of the exit tunnel (By similarity). Deleting residues 82 to 84 (the equivalent deletion in E.coli renders cells resistant to erythromycin) would probably cause the tip of the hairpin to penetrate into the tunnel.	+	[[https://www.uniprot.org/uniprot/RL22_THETH RL22_THETH]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome. This extension seems to form part of the wall of the exit tunnel (By similarity). Deleting residues 82 to 84 (the equivalent deletion in E.coli renders cells resistant to erythromycin) would probably cause the tip of the hairpin to penetrate into the tunnel.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:25, 18 December 2019

2019-12-18T14:25:13Z

←Older revision		Revision as of 14:25, 18 December 2019
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	==RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS==		==RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS==
-	<StructureSection load='1bxe' size='340' side='right' caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='1bxe' size='340' side='right'caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Large Structures]]
	[[Category: Aberg, A]]		[[Category: Aberg, A]]
	[[Category: Al-Karadaghi, S]]		[[Category: Al-Karadaghi, S]]

OCA at 05:24, 8 March 2018

2018-03-08T05:24:47Z

←Older revision		Revision as of 05:24, 8 March 2018
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	<StructureSection load='1bxe' size='340' side='right' caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1bxe' size='340' side='right' caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bx/1bxe_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bx/1bxe_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 36:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Aberg, A]]		[[Category: Aberg, A]]
	[[Category: Al-Karadaghi, S]]		[[Category: Al-Karadaghi, S]]

OCA at 06:16, 17 August 2017

2017-08-17T06:16:03Z

←Older revision		Revision as of 06:16, 17 August 2017
Line 1:		Line 1:
		+
	==RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS==		==RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS==
	<StructureSection load='1bxe' size='340' side='right' caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1bxe' size='340' side='right' caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://pdbe.org/1bxe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe 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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://pdbe.org/1bxe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bxe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bxe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Aberg, A]]		[[Category: Aberg, A]]
	[[Category: Al-Karadaghi, S]]		[[Category: Al-Karadaghi, S]]

OCA at 08:06, 11 September 2015

2015-09-11T08:06:48Z

←Older revision		Revision as of 08:06, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1bxe' size='340' side='right' caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='1bxe' size='340' side='right' caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bxe]] is a 1 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=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bxe]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe 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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://pdbe.org/1bxe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1bxe" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Aberg, A]]		[[Category: Aberg, A]]
	[[Category: Al-Karadaghi, S]]		[[Category: Al-Karadaghi, S]]

OCA at 13:38, 25 December 2014

2014-12-25T13:38:49Z

←Older revision		Revision as of 13:38, 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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe 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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RL22_THETH RL22_THETH]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity). The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome. This extension seems to form part of the wall of the exit tunnel (By similarity). Deleting residues 82 to 84 (the equivalent deletion in E.coli renders cells resistant to erythromycin) would probably cause the tip of the hairpin to penetrate into the tunnel.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 09:20, 22 December 2014

2014-12-22T09:20:54Z

←Older revision		Revision as of 09:20, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bxe]] is a 1 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=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bxe]] is a 1 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=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe 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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Aberg, A.]]	+	[[Category: Aberg, A]]
-	[[Category: Al-Karadaghi, S.]]	+	[[Category: Al-Karadaghi, S]]
-	[[Category: Davydova, N.]]	+	[[Category: Davydova, N]]
-	[[Category: Garber, M.]]	+	[[Category: Garber, M]]
-	[[Category: Liljas, A.]]	+	[[Category: Liljas, A]]
-	[[Category: Nevskaya, N.]]	+	[[Category: Nevskaya, N]]
-	[[Category: Nikonov, S.]]	+	[[Category: Nikonov, S]]
-	[[Category: Nikulin, A.]]	+	[[Category: Nikulin, A]]
-	[[Category: Unge, J.]]	+	[[Category: Unge, J]]
	[[Category: Antibiotics resistance]]		[[Category: Antibiotics resistance]]
	[[Category: Protein synthesis]]		[[Category: Protein synthesis]]

OCA at 09:46, 13 August 2014

2014-08-13T09:46:52Z

←Older revision		Revision as of 09:46, 13 August 2014
Line 1:		Line 1:
-	[[~~Image:~~1bxe.~~png~~\|~~left~~\|200px]]	+	==RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS==
		+	<StructureSection load='1bxe' size='340' side='right' caption='[[1bxe]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1bxe]] is a 1 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=1BXE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BXE FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1bxe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bxe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bxe RCSB], [http://www.ebi.ac.uk/pdbsum/1bxe PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bx/1bxe_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Background:. The ribosomal protein L22 is one of five proteins necessary for the formation of an early folding intermediate of the 23S rRNA. L22 has been found on the cytoplasmic side of the 50S ribosomal subunit. It can also be labeled by an erythromycin derivative bound close to the peptidyl-transfer center at the interface side of the 50S subunit, and the amino acid sequence of an erythromycin-resistant mutant is known. Knowing the structure of the protein may resolve this apparent conflict regarding the location of L22 on the ribosome. Results:. The structure of Thermus thermophilus L22 was solved using X-ray crystallography. L22 consists of a small alpha+beta domain and a protruding beta hairpin that is 30 A long. A large part of the surface area of the protein has the potential to be involved in interactions with rRNA. A structural similarity to other RNA-binding proteins is found, possibly indicating a common evolutionary origin. Conclusions:. The extensive surface area of L22 has the characteristics of an RNA-binding protein, consistent with its role in the folding of the 23S rRNA. The erythromycin-resistance conferring mutation is located in the protruding beta hairpin that is postulated to be important in L22-rRNA interactions. This region of the protein might be at the erythromycin-binding site close to the peptidyl transferase center, whereas the opposite end may be exposed to the cytoplasm.

-	~~{{STRUCTURE_1bxe\| PDB=1bxe \| SCENE= }}~~	+	The crystal structure of ribosomal protein L22 from Thermus thermophilus: insights into the mechanism of erythromycin resistance.,Unge J, berg A, Al-Kharadaghi S, Nikulin A, Nikonov S, Davydova N, Nevskaya N, Garber M, Liljas A Structure. 1998 Dec 15;6(12):1577-86. PMID:9862810<ref>PMID:9862810</ref>

-	~~===RIBOSOMAL PROTEIN L22 FROM THERMUS THERMOPHILUS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9862810}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1bxe]] is~~ a ~~1 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=1BXE OCA].~~	+

	==See Also==		==See Also==
	*[[Ribosomal protein L22\|Ribosomal protein L22]]		*[[Ribosomal protein L22\|Ribosomal protein L22]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009862810<~~/~~ref~~><~~ref group="xtra">PMID:015048824</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Aberg, A.]]		[[Category: Aberg, A.]]

OCA at 17:20, 20 October 2012

2012-10-20T17:20:21Z

←Older revision		Revision as of 17:20, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1bxe]] is a 1 chain structure ~~of [[Ribosomal protein L22]]~~ 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=1BXE OCA].	+	[[1bxe]] is a 1 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=1BXE OCA].

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