4qcx - Revision history

OCA: Redirecting to 1vy6

OCA — Wed, 10 Dec 2014 15:50:24 GMT

Redirecting to 1vy6

←Older revision		Revision as of 15:50, 10 December 2014
Line 1:		Line 1:
-	==Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site. This entry contains the 50S subunit of the second 70S ribosome in the ASU.==	+	#REDIRECT [[1vy6]] This PDB entry is obsolete and replaced by 1vy6
-	~~<StructureSection load='4qcx' size='340' side='right' caption='~~[[~~4qcx]], [[Resolution\|resolution]] 2.90Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[4qcx~~]] is a 30 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=4QCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QCX FirstGlance]. <br>	+
-	~~</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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">[[4qcu\|4qcu]], [[4qcv\|4qcv]], [[4qcw\|4qcw]]</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=4qcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qcx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qcx RCSB], [http://www.ebi.ac.uk/pdbsum/4qcx PDBsum]</span></td></tr>	+
-	~~<table>~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~During peptide-bond formation on the ribosome, the alpha-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened~~ by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-A resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.	+
-		+
-	A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.,Polikanov YS, Steitz TA, Innis CA Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179<ref>PMID:25132179</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Thermus thermophilus]]~~	+
-	~~[[Category: Innis, C A.]]~~	+
-	~~[[Category: Polikanov, Y S.]]~~	+
-	~~[[Category: Steitz, T A.]]~~	+
-	~~[[Category: 70]]~~	+
-	~~[[Category: Acylated trna]]~~	+
-	~~[[Category: Cytidine-puromycin]]~~	+
-	~~[[Category: Peptydil transfer reaction]]~~	+
-	~~[[Category: Proton transfer mechanism]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Translation]]~~	+

OCA at 03:18, 4 September 2014

OCA — Thu, 04 Sep 2014 03:18:44 GMT

←Older revision		Revision as of 03:18, 4 September 2014
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	<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=4qcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qcx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qcx RCSB], [http://www.ebi.ac.uk/pdbsum/4qcx PDBsum]</span></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=4qcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qcx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qcx RCSB], [http://www.ebi.ac.uk/pdbsum/4qcx PDBsum]</span></td></tr>
	<table>		<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	During peptide-bond formation on the ribosome, the alpha-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-A resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.
		+
		+	A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.,Polikanov YS, Steitz TA, Innis CA Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179<ref>PMID:25132179</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:35, 20 August 2014

OCA — Wed, 20 Aug 2014 16:35:40 GMT

←Older revision		Revision as of 16:35, 20 August 2014
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-	~~'''Unreleased structure'''~~	+	==Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site. This entry contains the 50S subunit of the second 70S ribosome in the ASU.==
-		+	<StructureSection load='4qcx' size='340' side='right' caption='[[4qcx]], [[Resolution\|resolution]] 2.90Å' scene=''>
-	~~The entry 4qcx is ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4qcx]] is a 30 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=4QCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QCX FirstGlance]. <br>
-	~~Authors: Polikanov, Y.S., Steitz, T.A., Innis, C.A.~~	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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">[[4qcu\|4qcu]], [[4qcv\|4qcv]], [[4qcw\|4qcw]]</td></tr>
-	~~Description:~~ Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site. This entry contains the 50S subunit of the second 70S ribosome.	+	<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=4qcx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qcx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qcx RCSB], [http://www.ebi.ac.uk/pdbsum/4qcx PDBsum]</span></td></tr>
		+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Thermus thermophilus]]
		+	[[Category: Innis, C A.]]
		+	[[Category: Polikanov, Y S.]]
		+	[[Category: Steitz, T A.]]
		+	[[Category: 70]]
		+	[[Category: Acylated trna]]
		+	[[Category: Cytidine-puromycin]]
		+	[[Category: Peptydil transfer reaction]]
		+	[[Category: Proton transfer mechanism]]
		+	[[Category: Ribosome]]
		+	[[Category: Translation]]

OCA at 01:05, 7 August 2014

OCA — Thu, 07 Aug 2014 01:05:48 GMT

←Older revision		Revision as of 01:05, 7 August 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Polikanov, Y.S., Steitz, T.A., Innis, C.A.		Authors: Polikanov, Y.S., Steitz, T.A., Innis, C.A.

	Description: Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site. This entry contains the 50S subunit of the second 70S ribosome.		Description: Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site. This entry contains the 50S subunit of the second 70S ribosome.

OCA at 08:29, 28 May 2014

OCA — Wed, 28 May 2014 08:29:36 GMT

←Older revision		Revision as of 08:29, 28 May 2014
Line 3:		Line 3:
	The entry 4qcx is ON HOLD		The entry 4qcx is ON HOLD

-	Authors: Polikanov, ~~Yury~~ S., Steitz, ~~Thomas~~ A., Innis, C. ~~Axel~~	+	Authors: Polikanov, Y.S., Steitz, T.A., Innis, C.A.

-	Description: Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site	+	Description: Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site. This entry contains the 50S subunit of the second 70S ribosome.

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

OCA — Wed, 21 May 2014 08:18:21 GMT

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

←Older revision

Revision as of 08:18, 21 May 2014

OCA: New page: '''Unreleased structure''' The entry 4qcx is ON HOLD Authors: Polikanov, Yury S., Steitz, Thomas A., Innis, C. Axel Description: Crystal structure of the Thermus thermophilus 70S ribos...

OCA — Wed, 21 May 2014 08:18:19 GMT

New page: '''Unreleased structure''' The entry 4qcx is ON HOLD Authors: Polikanov, Yury S., Steitz, Thomas A., Innis, C. Axel Description: Crystal structure of the Thermus thermophilus 70S ribos...

New page

'''Unreleased structure'''

The entry 4qcx is ON HOLD

Authors: Polikanov, Yury S., Steitz, Thomas A., Innis, C. Axel

Description: Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site