6swe - Revision history

OCA at 06:19, 11 April 2020

2020-04-11T06:19:25Z

←Older revision		Revision as of 06:19, 11 April 2020
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	<SX load='6swe' size='340' side='right' viewer='molstar' caption='[[6swe]], [[Resolution\|resolution]] 3.10Å' scene=''>		<SX load='6swe' size='340' side='right' viewer='molstar' caption='[[6swe]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6swe]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_(strain_ge5_/_orsay) Pyrococcus abyssi (strain ge5 / orsay)] and [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_ge5 Pyrococcus abyssi ge5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SWE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6SWE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6swe]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_(strain_ge5_/_orsay) Pyrococcus abyssi (strain ge5 / orsay)] and [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_ge5 Pyrococcus abyssi ge5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SWE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SWE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><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></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=B8H:'>B8H</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=B8H:'>B8H</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=6swe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6swe OCA], [http://pdbe.org/6swe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6swe RCSB], [http://www.ebi.ac.uk/pdbsum/6swe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6swe ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6swe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6swe OCA], [http://pdbe.org/6swe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6swe RCSB], [http://www.ebi.ac.uk/pdbsum/6swe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6swe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 00:55, 7 March 2020

2020-03-07T00:55:49Z

←Older revision		Revision as of 00:55, 7 March 2020
Line 1:		Line 1:

	==IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi==		==IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi==
-	<~~StructureSection~~ load='6swe' size='340' side='right'caption='[[6swe]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<SX load='6swe' size='340' side='right' viewer='molstar' caption='[[6swe]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6swe]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_(strain_ge5_/_orsay) Pyrococcus abyssi (strain ge5 / orsay)] and [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_ge5 Pyrococcus abyssi ge5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SWE FirstGlance]. <br>		<table><tr><td colspan='2'>[[6swe]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_(strain_ge5_/_orsay) Pyrococcus abyssi (strain ge5 / orsay)] and [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_ge5 Pyrococcus abyssi ge5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SWE FirstGlance]. <br>
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	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/RS14Z_PYRAB RS14Z_PYRAB]] Binds 16S rRNA, required for the assembly of 30S particles. [[http://www.uniprot.org/uniprot/RS19E_PYRAB RS19E_PYRAB]] May be involved in maturation of the 30S ribosomal subunit~~. [[http://www.uniprot.org/uniprot/RS3_PYRAB RS3_PYRAB]] Binds the lower part of the 30S subunit head~~. [[http://www.uniprot.org/uniprot/RS7_PYRAB RS7_PYRAB]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. [[http://www.uniprot.org/uniprot/IF1A_PYRAB IF1A_PYRAB]] Seems to be required for maximal rate of protein biosynthesis. Enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA(I) to 40 S ribosomal subunits (By similarity). [[http://www.uniprot.org/uniprot/RS19_PYRAB RS19_PYRAB]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS10_PYRAB RS10_PYRAB]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL7A_PYRAB RL7A_PYRAB]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs. [[http://www.uniprot.org/uniprot/RS13_PYRAB RS13_PYRAB]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement.	+	[[http://www.uniprot.org/uniprot/RS14Z_PYRAB RS14Z_PYRAB]] Binds 16S rRNA, required for the assembly of 30S particles. [[http://www.uniprot.org/uniprot/RS19E_PYRAB RS19E_PYRAB]] May be involved in maturation of the 30S ribosomal subunit. [[http://www.uniprot.org/uniprot/RS7_PYRAB RS7_PYRAB]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. [[http://www.uniprot.org/uniprot/RS3_PYRAB RS3_PYRAB]] Binds the lower part of the 30S subunit head. [[http://www.uniprot.org/uniprot/IF1A_PYRAB IF1A_PYRAB]] Seems to be required for maximal rate of protein biosynthesis. Enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA(I) to 40 S ribosomal subunits (By similarity). [[http://www.uniprot.org/uniprot/RS19_PYRAB RS19_PYRAB]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS10_PYRAB RS10_PYRAB]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL7A_PYRAB RL7A_PYRAB]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs. [[http://www.uniprot.org/uniprot/RS13_PYRAB RS13_PYRAB]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Pyrococcus abyssi ge5]]		[[Category: Pyrococcus abyssi ge5]]

OCA at 06:36, 19 February 2020

2020-02-19T06:36:36Z

←Older revision		Revision as of 06:36, 19 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6swe is ~~ON HOLD~~	+	==IC2 head of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi==
		+	<StructureSection load='6swe' size='340' side='right'caption='[[6swe]], [[Resolution\|resolution]] 3.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6swe]] is a 15 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_(strain_ge5_/_orsay) Pyrococcus abyssi (strain ge5 / orsay)] and [http://en.wikipedia.org/wiki/Pyrococcus_abyssi_ge5 Pyrococcus abyssi ge5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SWE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SWE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><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></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=B8H:'>B8H</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</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=6swe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6swe OCA], [http://pdbe.org/6swe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6swe RCSB], [http://www.ebi.ac.uk/pdbsum/6swe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6swe ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RS14Z_PYRAB RS14Z_PYRAB]] Binds 16S rRNA, required for the assembly of 30S particles. [[http://www.uniprot.org/uniprot/RS19E_PYRAB RS19E_PYRAB]] May be involved in maturation of the 30S ribosomal subunit. [[http://www.uniprot.org/uniprot/RS3_PYRAB RS3_PYRAB]] Binds the lower part of the 30S subunit head. [[http://www.uniprot.org/uniprot/RS7_PYRAB RS7_PYRAB]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. [[http://www.uniprot.org/uniprot/IF1A_PYRAB IF1A_PYRAB]] Seems to be required for maximal rate of protein biosynthesis. Enhances ribosome dissociation into subunits and stabilizes the binding of the initiator Met-tRNA(I) to 40 S ribosomal subunits (By similarity). [[http://www.uniprot.org/uniprot/RS19_PYRAB RS19_PYRAB]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [[http://www.uniprot.org/uniprot/RS10_PYRAB RS10_PYRAB]] Involved in the binding of tRNA to the ribosomes. [[http://www.uniprot.org/uniprot/RL7A_PYRAB RL7A_PYRAB]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, the RNA component of RNase P, box H/ACA, box C/D and box C'/D' sRNAs. [[http://www.uniprot.org/uniprot/RS13_PYRAB RS13_PYRAB]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Archaeal translation initiation occurs within a macromolecular complex containing the small ribosomal subunit (30S) bound to mRNA, initiation factors aIF1, aIF1A and the ternary complex aIF2:GDPNP:Met-tRNAi(Met). Here, we determine the cryo-EM structure of a 30S:mRNA:aIF1A:aIF2:GTP:Met-tRNAi(Met) complex from Pyrococcus abyssi at 3.2 A resolution. It highlights archaeal features in ribosomal proteins and rRNA modifications. We find an aS21 protein, at the location of eS21 in eukaryotic ribosomes. Moreover, we identify an N-terminal extension of archaeal eL41 contacting the P site. We characterize 34 N(4)-acetylcytidines distributed throughout 16S rRNA, likely contributing to hyperthermostability. Without aIF1, the 30S head is stabilized and initiator tRNA is tightly bound to the P site. A network of interactions involving tRNA, mRNA, rRNA modified nucleotides and C-terminal tails of uS9, uS13 and uS19 is observed. Universal features and domain-specific idiosyncrasies of translation initiation are discussed in light of ribosomal structures from representatives of each domain of life.

-	~~Authors~~:	+	Cryo-EM study of an archaeal 30S initiation complex gives insights into evolution of translation initiation.,Coureux PD, Lazennec-Schurdevin C, Bourcier S, Mechulam Y, Schmitt E Commun Biol. 2020 Feb 6;3(1):58. doi: 10.1038/s42003-020-0780-0. PMID:32029867<ref>PMID:32029867</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6swe" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrococcus abyssi ge5]]
		+	[[Category: Coureux, P D]]
		+	[[Category: Mechulam, Y]]
		+	[[Category: Schmitt, E]]
		+	[[Category: Archaea]]
		+	[[Category: Cryo-em]]
		+	[[Category: Evolution]]
		+	[[Category: Ribosome]]
		+	[[Category: Rrna modification]]
		+	[[Category: Translation initiation]]
		+	[[Category: Trna]]

OCA: Protected "6swe" [edit=sysop:move=sysop]

2019-10-02T07:55:35Z

Protected "6swe" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:55, 2 October 2019

OCA: New page: '''Unreleased structure''' The entry 6swe is ON HOLD Authors: Description: Category: Unreleased Structures

2019-10-02T07:55:33Z

New page: '''Unreleased structure''' The entry 6swe is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6swe is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]