7ode - Revision history

OCA at 09:00, 14 July 2024

2024-07-14T09:00:15Z

← Older revision		Revision as of 09:00, 14 July 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ode]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ODE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ODE FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ode]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ODE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ODE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MEQ:N5-METHYLGLUTAMINE'>MEQ</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 2.84Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MEQ:N5-METHYLGLUTAMINE'>MEQ</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=7ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ode OCA], [https://pdbe.org/7ode PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ode RCSB], [https://www.ebi.ac.uk/pdbsum/7ode PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ode 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=7ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ode OCA], [https://pdbe.org/7ode PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ode RCSB], [https://www.ebi.ac.uk/pdbsum/7ode PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ode ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 7ode" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7ode" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Ribosome 3D structures\|Ribosome 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:17, 14 December 2022

2022-12-14T10:17:56Z

← Older revision		Revision as of 10:17, 14 December 2022
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7ode is ~~ON HOLD~~ ~~until Paper~~ Publication		==E. coli 50S ribosome LiCl core particle==
			<StructureSection load='7ode' size='340' side='right'caption='[[7ode]], [[Resolution\|resolution]] 2.84Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[7ode]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ODE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ODE FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MA:2-METHYLADENOSINE-5-MONOPHOSPHATE'>2MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=G7M:N7-METHYL-GUANOSINE-5-MONOPHOSPHATE'>G7M</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MEQ:N5-METHYLGLUTAMINE'>MEQ</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</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=7ode FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ode OCA], [https://pdbe.org/7ode PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ode RCSB], [https://www.ebi.ac.uk/pdbsum/7ode PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ode ProSAT]</span></td></tr>
			</table>
			== Function ==
			[https://www.uniprot.org/uniprot/RL2_ECOLI RL2_ECOLI] One of the primary rRNA binding proteins. Located near the base of the L1 stalk, it is probably also mobile. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is highly controversial.[HAMAP-Rule:MF_01320_B] In the E.coli 70S ribosome in the initiation state it has been modeled to make several contacts with the 16S rRNA (forming bridge B7b, PubMed:12809609); these contacts are broken in the model with bound EF-G.[HAMAP-Rule:MF_01320_B]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Ribosomes are complex ribonucleoprotein particles. Purified 50S ribosomes subjected to high-salt wash, removing a subset of ribosomal proteins (r-proteins), were shown as competent for in vitro assembly into functional 50S subunits. Here, we used cryo-EM to determine the structures of such LiCl core particles derived from E. coli 50S subunits. A wide range of complexes with large variations in the extent of the ordered 23S rRNA and the occupancy of r-proteins were resolved to between 2.8 A and 9 A resolution. Many of these particles showed high similarity to in vivo and in vitro assembly intermediates, supporting the inherent stability or metastability of these states. Similar to states in early ribosome assembly, the main class showed an ordered density for the particle base around the exit tunnel, with domain V and the 3'-half of domain IV disordered. In addition, smaller core particles were discovered, where either domain II or IV was unfolded. Our data support a multi-pathway in vitro disassembly process, similar but reverse to assembly. Dependencies between complex tertiary RNA structures and RNA-protein interactions were observed, where protein extensions dissociated before the globular domains. We observed the formation of a non-native RNA structure upon protein dissociation, demonstrating that r-proteins stabilize native RNA structures and prevent non-native interactions also after folding.

	~~Authors:~~ Larsson, D.S~~.D.~~, Selmer, M.		Structural Consequences of Deproteinating the 50S Ribosome.,Larsson DSD, Kanchugal P S, Selmer M Biomolecules. 2022 Oct 31;12(11):1605. doi: 10.3390/biom12111605. PMID:36358955<ref>PMID:36358955</ref>

	~~Description~~: E. coli ~~50S ribosome LiCl core particle~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: ~~Selmer, M~~]]		<div class="pdbe-citations 7ode" style="background-color:#fffaf0;"></div>
	[[Category: ~~Larsson, D.S.D~~]]		== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Escherichia coli K-12]]
			[[Category: Large Structures]]
			[[Category: Larsson DSD]]
			[[Category: Selmer M]]

OCA at 13:44, 17 June 2021

2021-06-17T13:44:16Z

← Older revision		Revision as of 13:44, 17 June 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 7ode is ON HOLD		The entry 7ode is ON HOLD until Paper Publication

	Authors: Larsson, D.S.D., Selmer, M.		Authors: Larsson, D.S.D., Selmer, M.
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	Description: E. coli 50S ribosome LiCl core particle		Description: E. coli 50S ribosome LiCl core particle
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
			[[Category: Selmer, M]]
	[[Category: Larsson, D.S.D]]		[[Category: Larsson, D.S.D]]
	~~[[Category: Selmer, M]]~~

OCA: Protected "7ode" [edit=sysop:move=sysop]

2021-05-05T07:38:58Z

Protected "7ode" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:38, 5 May 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7ode is ON HOLD Authors: Larsson, D.S.D., Selmer, M. Description: E. coli 50S ribosome LiCl core particle Category: Unreleased Structures [[Cat...

2021-05-05T07:38:57Z

New page: '''Unreleased structure''' The entry 7ode is ON HOLD Authors: Larsson, D.S.D., Selmer, M. Description: E. coli 50S ribosome LiCl core particle Category: Unreleased Structures [[Cat...

New page

'''Unreleased structure'''

The entry 7ode is ON HOLD

Authors: Larsson, D.S.D., Selmer, M.

Description: E. coli 50S ribosome LiCl core particle
[[Category: Unreleased Structures]]
[[Category: Larsson, D.S.D]]
[[Category: Selmer, M]]