6swd - Revision history

OCA at 06:19, 11 April 2020

OCA — Sat, 11 Apr 2020 06:19:12 GMT

←Older revision		Revision as of 06:19, 11 April 2020
Line 3:		Line 3:
	<SX load='6swd' size='340' side='right' viewer='molstar' caption='[[6swd]], [[Resolution\|resolution]] 3.20Å' scene=''>		<SX load='6swd' size='340' side='right' viewer='molstar' caption='[[6swd]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6swd]] is a 18 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=6SWD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6SWD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6swd]] is a 18 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=6SWD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6SWD 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=5HM:5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HM</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=LHH:'>LHH</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=5HM:5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HM</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=LHH:'>LHH</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=6swd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6swd OCA], [http://pdbe.org/6swd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6swd RCSB], [http://www.ebi.ac.uk/pdbsum/6swd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6swd 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=6swd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6swd OCA], [http://pdbe.org/6swd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6swd RCSB], [http://www.ebi.ac.uk/pdbsum/6swd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6swd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 00:55, 7 March 2020

OCA — Sat, 07 Mar 2020 00:55:46 GMT

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

	==IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi==		==IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi==
-	<~~StructureSection~~ load='6swd' size='340' side='right'caption='[[6swd]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<SX load='6swd' size='340' side='right' viewer='molstar' caption='[[6swd]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6swd]] is a 18 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=6SWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SWD FirstGlance]. <br>		<table><tr><td colspan='2'>[[6swd]] is a 18 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=6SWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SWD FirstGlance]. <br>
Line 22:		Line 22:
	<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

OCA — Wed, 19 Feb 2020 06:36:53 GMT

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

-	~~The entry~~ 6swd is ~~ON HOLD~~	+	==IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi==
		+	<StructureSection load='6swd' size='340' side='right'caption='[[6swd]], [[Resolution\|resolution]] 3.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6swd]] is a 18 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=6SWD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SWD 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=5HM:5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HM</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=LHH:'>LHH</scene>, <scene name='pdbligand=MA6:6N-DIMETHYLADENOSINE-5-MONOPHOSHATE'>MA6</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</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=6swd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6swd OCA], [http://pdbe.org/6swd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6swd RCSB], [http://www.ebi.ac.uk/pdbsum/6swd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6swd ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RS11_PYRAB RS11_PYRAB]] Located on the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS5_PYRAB RS5_PYRAB]] With S4 and S12 plays an important role in translational accuracy. [[http://www.uniprot.org/uniprot/RS8_PYRAB RS8_PYRAB]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit. [[http://www.uniprot.org/uniprot/RS12_PYRAB RS12_PYRAB]] With S4 and S5 plays an important role in translational accuracy. Located at the interface of the 30S and 50S subunits. [[http://www.uniprot.org/uniprot/RS17_PYRAB RS17_PYRAB]] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA.[HAMAP-Rule:MF_01345] [[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/RS4_PYRAB RS4_PYRAB]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy.
		+	<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 6swd" 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 "6swd" [edit=sysop:move=sysop]

OCA — Wed, 02 Oct 2019 07:55:31 GMT

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

←Older revision

Revision as of 07:55, 2 October 2019

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

OCA — Wed, 02 Oct 2019 07:55:29 GMT

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

New page

'''Unreleased structure'''

The entry 6swd is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]