4q7j - Revision history

OCA at 15:04, 8 November 2023

OCA — Wed, 08 Nov 2023 15:04:24 GMT

←Older revision		Revision as of 15:04, 8 November 2023
Line 1:		Line 1:

	==Complex structure of viral RNA polymerase==		==Complex structure of viral RNA polymerase==
-	<StructureSection load='4q7j' size='340' side='right'caption='[[4q7j]]' scene=''>	+	<StructureSection load='4q7j' size='340' side='right'caption='[[4q7j]], [[Resolution\|resolution]] 2.90Å' 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=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q7j]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_virus_Qbeta Escherichia virus Qbeta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q7J 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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [https://pdbe.org/4q7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [https://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j ProSAT]</span></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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [https://pdbe.org/4q7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [https://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosomal protein S1, consisting of six contiguous OB-folds, is the largest ribosomal protein and is essential for translation initiation in Escherichia coli. S1 is also one of the three essential host-derived subunits of Qbeta replicase, together with EF-Tu and EF-Ts, for Qbeta RNA replication in E. coli. We analyzed the crystal structure of Qbeta replicase, consisting of the virus-encoded RNA-dependent RNA polymerase (beta-subunit), EF-Tu, EF-Ts and the N-terminal half of S1, which is capable of initiating Qbeta RNA replication. Structural and biochemical studies revealed that the two N-terminal OB-folds of S1 anchor S1 onto the beta-subunit, and the third OB-fold is mobile and protrudes beyond the surface of the beta-subunit. The third OB-fold mainly interacts with a specific RNA fragment derived from the internal region of Qbeta RNA, and its RNA-binding ability is required for replication initiation of Qbeta RNA. Thus, the third mobile OB-fold of S1, which is spatially anchored near the surface of the beta-subunit, primarily recruits the Qbeta RNA toward the beta-subunit, leading to the specific and efficient replication initiation of Qbeta RNA, and S1 functions as a replication initiation factor, beyond its established function in protein synthesis.
		+
		+	Molecular insights into replication initiation by Qbeta replicase using ribosomal protein S1.,Takeshita D, Yamashita S, Tomita K Nucleic Acids Res. 2014 Aug 13. pii: gku745. PMID:25122749<ref>PMID:25122749</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4q7j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]		*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	*[[Ribosomal protein S1\|Ribosomal protein S1]]		*[[Ribosomal protein S1\|Ribosomal protein S1]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli K-12]]
		+	[[Category: Escherichia virus Qbeta]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Takeshita D]]		[[Category: Takeshita D]]

OCA at 10:54, 31 August 2022

OCA — Wed, 31 Aug 2022 10:54:34 GMT

←Older revision		Revision as of 10:54, 31 August 2022
Line 1:		Line 1:

	==Complex structure of viral RNA polymerase==		==Complex structure of viral RNA polymerase==
-	<StructureSection load='4q7j' size='340' side='right'caption='[[4q7j]]~~, [[Resolution\|resolution]] 2.90Å~~' scene=''>	+	<StructureSection load='4q7j' size='340' side='right'caption='[[4q7j]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[4q7j]] is a 8 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>~~	+	</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [https://pdbe.org/4q7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [https://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3agp\|3agp]], [[3agq\|3agq]]</div></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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [https://pdbe.org/4q7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [https://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/RS1_ECOLI RS1_ECOLI]] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. [[https://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI]] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050] [[https://www.uniprot.org/uniprot/EFTU1_ECOLI EFTU1_ECOLI]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ribosomal protein S1, consisting of six contiguous OB-folds, is the largest ribosomal protein and is essential for translation initiation in Escherichia coli. S1 is also one of the three essential host-derived subunits of Qbeta replicase, together with EF-Tu and EF-Ts, for Qbeta RNA replication in E. coli. We analyzed the crystal structure of Qbeta replicase, consisting of the virus-encoded RNA-dependent RNA polymerase (beta-subunit), EF-Tu, EF-Ts and the N-terminal half of S1, which is capable of initiating Qbeta RNA replication. Structural and biochemical studies revealed that the two N-terminal OB-folds of S1 anchor S1 onto the beta-subunit, and the third OB-fold is mobile and protrudes beyond the surface of the beta-subunit. The third OB-fold mainly interacts with a specific RNA fragment derived from the internal region of Qbeta RNA, and its RNA-binding ability is required for replication initiation of Qbeta RNA. Thus, the third mobile OB-fold of S1, which is spatially anchored near the surface of the beta-subunit, primarily recruits the Qbeta RNA toward the beta-subunit, leading to the specific and efficient replication initiation of Qbeta RNA, and S1 functions as a replication initiation factor, beyond its established function in protein synthesis.
-
-	Molecular insights into replication initiation by Qbeta replicase using ribosomal protein S1.,Takeshita D, Yamashita S, Tomita K Nucleic Acids Res. 2014 Aug 13. pii: gku745. PMID:25122749<ref>PMID:25122749</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4q7j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]		*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	*[[Ribosomal protein S1\|Ribosomal protein S1]]		*[[Ribosomal protein S1\|Ribosomal protein S1]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Takeshita, D]]	+	[[Category: Takeshita D]]
-	~~[[Category: Rna binding motif]]~~	+
-	~~[[Category: Rna dependent rna polymerization]]~~	+
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Translation-transferase complex~~]]	+

OCA at 05:06, 25 August 2022

OCA — Thu, 25 Aug 2022 05:06:52 GMT

←Older revision		Revision as of 05:06, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='4q7j' size='340' side='right'caption='[[4q7j]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4q7j' size='340' side='right'caption='[[4q7j]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4q7j]] is a 8 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/Allolevivirus_subgroup_iii Allolevivirus subgroup iii] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q7j]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3agp\|3agp]], [[3agq\|3agq]]</td>~~</tr>~~	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3agp\|3agp]], [[3agq\|3agq]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tsf ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), tufA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [https://pdbe.org/4q7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [https://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j ProSAT]</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [~~http~~://pdbe.org/4q7j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RS1_ECOLI RS1_ECOLI]] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. [[~~http~~://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI]] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050] [[~~http~~://www.uniprot.org/uniprot/EFTU1_ECOLI EFTU1_ECOLI]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118]	+	[[https://www.uniprot.org/uniprot/RS1_ECOLI RS1_ECOLI]] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. [[https://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI]] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050] [[https://www.uniprot.org/uniprot/EFTU1_ECOLI EFTU1_ECOLI]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:

	==See Also==		==See Also==
-	*[[Elongation factor\|Elongation factor]]	+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	*[[Ribosomal protein S1\|Ribosomal protein S1]]		*[[Ribosomal protein S1\|Ribosomal protein S1]]
	== References ==		== References ==
Line 28:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Allolevivirus subgroup iii]]
-	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Takeshita, D]]		[[Category: Takeshita, D]]

OCA at 09:44, 24 April 2019

OCA — Wed, 24 Apr 2019 09:44:19 GMT

←Older revision		Revision as of 09:44, 24 April 2019
Line 1:		Line 1:

	==Complex structure of viral RNA polymerase==		==Complex structure of viral RNA polymerase==
-	<StructureSection load='4q7j' size='340' side='right' caption='[[4q7j]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='4q7j' size='340' side='right'caption='[[4q7j]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4q7j]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4q7j]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Allolevivirus_subgroup_iii Allolevivirus subgroup iii] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3agp\|3agp]], [[3agq\|3agq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3agp\|3agp]], [[3agq\|3agq]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tsf ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), tufA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), rpsA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [http://pdbe.org/4q7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [http://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j ProSAT]</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [http://pdbe.org/4q7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [http://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j ProSAT]</span></td></tr>
	</table>		</table>
Line 27:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Allolevivirus subgroup iii]]
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Takeshita, D]]		[[Category: Takeshita, D]]
	[[Category: Rna binding motif]]		[[Category: Rna binding motif]]

OCA at 07:50, 5 August 2016

OCA — Fri, 05 Aug 2016 07:50:33 GMT

←Older revision		Revision as of 07:50, 5 August 2016
Line 1:		Line 1:
		+
	==Complex structure of viral RNA polymerase==		==Complex structure of viral RNA polymerase==
	<StructureSection load='4q7j' size='340' side='right' caption='[[4q7j]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4q7j' size='340' side='right' caption='[[4q7j]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3agp\|3agp]], [[3agq\|3agq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3agp\|3agp]], [[3agq\|3agq]]</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [http://www.ebi.ac.uk/pdbsum/4q7j 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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [http://pdbe.org/4q7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [http://www.ebi.ac.uk/pdbsum/4q7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q7j 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 4q7j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Elongation factor\|Elongation factor]]
		+	*[[Ribosomal protein S1\|Ribosomal protein S1]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:03, 25 December 2014

OCA — Thu, 25 Dec 2014 17:03:00 GMT

←Older revision		Revision as of 17:03, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4q7j]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[4q7j]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3agp\|3agp]], [[3agq\|3agq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3agp\|3agp]], [[3agq\|3agq]]</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [http://www.ebi.ac.uk/pdbsum/4q7j 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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [http://www.ebi.ac.uk/pdbsum/4q7j PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RS1_ECOLI RS1_ECOLI]] Binds mRNA; thus facilitating recognition of the initiation point. It is needed to translate mRNA with a short Shine-Dalgarno (SD) purine-rich sequence. [[http://www.uniprot.org/uniprot/EFTS_ECOLI EFTS_ECOLI]] Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome.[HAMAP-Rule:MF_00050] [[http://www.uniprot.org/uniprot/EFTU1_ECOLI EFTU1_ECOLI]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] May play an important regulatory role in cell growth and in the bacterial response to nutrient deprivation.[HAMAP-Rule:MF_00118]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Takeshita, D.]]	+	[[Category: Takeshita, D]]
	[[Category: Rna binding motif]]		[[Category: Rna binding motif]]
	[[Category: Rna dependent rna polymerization]]		[[Category: Rna dependent rna polymerization]]
	[[Category: Rna polymerase]]		[[Category: Rna polymerase]]
	[[Category: Translation-transferase complex]]		[[Category: Translation-transferase complex]]

OCA at 08:45, 27 August 2014

OCA — Wed, 27 Aug 2014 08:45:15 GMT

←Older revision		Revision as of 08:45, 27 August 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Complex structure of viral RNA polymerase==
		+	<StructureSection load='4q7j' size='340' side='right' caption='[[4q7j]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4q7j]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q7J FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3agp\|3agp]], [[3agq\|3agq]]</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=4q7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4q7j RCSB], [http://www.ebi.ac.uk/pdbsum/4q7j PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosomal protein S1, consisting of six contiguous OB-folds, is the largest ribosomal protein and is essential for translation initiation in Escherichia coli. S1 is also one of the three essential host-derived subunits of Qbeta replicase, together with EF-Tu and EF-Ts, for Qbeta RNA replication in E. coli. We analyzed the crystal structure of Qbeta replicase, consisting of the virus-encoded RNA-dependent RNA polymerase (beta-subunit), EF-Tu, EF-Ts and the N-terminal half of S1, which is capable of initiating Qbeta RNA replication. Structural and biochemical studies revealed that the two N-terminal OB-folds of S1 anchor S1 onto the beta-subunit, and the third OB-fold is mobile and protrudes beyond the surface of the beta-subunit. The third OB-fold mainly interacts with a specific RNA fragment derived from the internal region of Qbeta RNA, and its RNA-binding ability is required for replication initiation of Qbeta RNA. Thus, the third mobile OB-fold of S1, which is spatially anchored near the surface of the beta-subunit, primarily recruits the Qbeta RNA toward the beta-subunit, leading to the specific and efficient replication initiation of Qbeta RNA, and S1 functions as a replication initiation factor, beyond its established function in protein synthesis.

-	~~The entry 4q7j is ON HOLD until Paper Publication~~	+	Molecular insights into replication initiation by Qbeta replicase using ribosomal protein S1.,Takeshita D, Yamashita S, Tomita K Nucleic Acids Res. 2014 Aug 13. pii: gku745. PMID:25122749<ref>PMID:25122749</ref>

-	~~Authors~~: Takeshita, D.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Complex structure of viral RNA~~ polymerase	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Takeshita, D.]]
		+	[[Category: Rna binding motif]]
		+	[[Category: Rna dependent rna polymerization]]
		+	[[Category: Rna polymerase]]
		+	[[Category: Translation-transferase complex]]

OCA at 14:33, 20 August 2014

OCA — Wed, 20 Aug 2014 14:33:29 GMT

←Older revision		Revision as of 14:33, 20 August 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4q7j is ON HOLD	+	The entry 4q7j is ON HOLD until Paper Publication

	Authors: Takeshita, D.		Authors: Takeshita, D.

	Description: Complex structure of viral RNA polymerase		Description: Complex structure of viral RNA polymerase

OCA: Protected "4q7j" [edit=sysop:move=sysop]

OCA — Wed, 07 May 2014 07:49:40 GMT

Protected "4q7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:49, 7 May 2014

OCA: New page: '''Unreleased structure''' The entry 4q7j is ON HOLD Authors: Takeshita, D. Description: Complex structure of viral RNA polymerase

OCA — Wed, 07 May 2014 07:49:39 GMT

New page: '''Unreleased structure''' The entry 4q7j is ON HOLD Authors: Takeshita, D. Description: Complex structure of viral RNA polymerase

New page

'''Unreleased structure'''

The entry 4q7j is ON HOLD

Authors: Takeshita, D.

Description: Complex structure of viral RNA polymerase