7pha - Revision history

OCA at 09:04, 17 October 2024

2024-10-17T09:04:26Z

← Older revision		Revision as of 09:04, 17 October 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7pha]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycoplasma_pneumoniae_M129 Mycoplasma pneumoniae M129]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PHA FirstGlance]. <br>		<table><tr><td colspan='2'>[[7pha]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycoplasma_pneumoniae_M129 Mycoplasma pneumoniae M129]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PHA 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=7pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pha OCA], [https://pdbe.org/7pha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pha RCSB], [https://www.ebi.ac.uk/pdbsum/7pha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pha ProSAT]</span></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]] 8.5Å</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=7pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pha OCA], [https://pdbe.org/7pha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pha RCSB], [https://www.ebi.ac.uk/pdbsum/7pha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pha ProSAT]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	~~[https://www.uniprot.org/uniprot/RL34_MYCPN RL34_MYCPN]~~
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells(1). Here we use advances in cryo-electron tomography and sub-tomogram analysis(2,3) to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes(4). By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.		Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells(1). Here we use advances in cryo-electron tomography and sub-tomogram analysis(2,3) to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes(4). By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.

	Visualizing translation dynamics at atomic detail inside a bacterial cell.,Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J Nature. 2022 Oct;610(7930):205-211. doi: 10.1038/s41586-022-05255-2. Epub 2022, Sep 28. PMID:36171285<ref>PMID:36171285</ref>		Visualizing translation dynamics at atomic detail inside a bacterial cell.,Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J Nature. 2022 Oct;610(7930):205-211. doi: 10.1038/s41586-022-05255-2. Epub 2022 , Sep 28. PMID:36171285<ref>PMID:36171285</ref>

	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 7pha" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7pha" style="background-color:#fffaf0;"></div>

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

OCA at 19:31, 19 October 2022

2022-10-19T19:31:27Z

← Older revision		Revision as of 19:31, 19 October 2022
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	====		==70S ribosome with EF-Tu-tRNA and P-site tRNA in chloramphenicol-treated Mycoplasma pneumoniae cells==
	<StructureSection load='7pha' size='340' side='right'caption='[[7pha]]' scene=''>		<StructureSection load='7pha' size='340' side='right'caption='[[7pha]], [[Resolution\|resolution]] 8.50Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>		<table><tr><td colspan='2'>[[7pha]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycoplasma_pneumoniae_M129 Mycoplasma pneumoniae M129]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PHA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PHA 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=7pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pha OCA], [https://pdbe.org/7pha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pha RCSB], [https://www.ebi.ac.uk/pdbsum/7pha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pha ProSAT]</span></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=7pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pha OCA], [https://pdbe.org/7pha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pha RCSB], [https://www.ebi.ac.uk/pdbsum/7pha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pha ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/RL34_MYCPN RL34_MYCPN]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Translation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells(1). Here we use advances in cryo-electron tomography and sub-tomogram analysis(2,3) to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes(4). By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.

			Visualizing translation dynamics at atomic detail inside a bacterial cell.,Xue L, Lenz S, Zimmermann-Kogadeeva M, Tegunov D, Cramer P, Bork P, Rappsilber J, Mahamid J Nature. 2022 Oct;610(7930):205-211. doi: 10.1038/s41586-022-05255-2. Epub 2022, Sep 28. PMID:36171285<ref>PMID:36171285</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 7pha" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Z-disk~~]]		[[Category: Mycoplasma pneumoniae M129]]
			[[Category: Lenz S]]
			[[Category: Mahamid J]]
			[[Category: Rappsilber J]]
			[[Category: Xue L]]

OCA at 07:57, 25 May 2022

2022-05-25T07:57:07Z

← Older revision		Revision as of 07:57, 25 May 2022
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	~~'''Unreleased structure'''~~

	~~The entry~~ 7pha ~~is ON HOLD until Paper Publication~~		====
			<StructureSection load='7pha' size='340' side='right'caption='[[7pha]]' scene=''>
	~~Authors~~: ~~Xue, L~~.~~, Lenz, S~~.~~, Rappsilber, J~~.~~, Mahamid, J~~.		== Structural highlights ==
			<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
	~~Description~~: ~~70S ribosome with EF-Tu-tRNA and P-site tRNA in chloramphenicol-treated Mycoplasma pneumoniae cells~~		</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=7pha FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pha OCA], [https://pdbe.org/7pha PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pha RCSB], [https://www.ebi.ac.uk/pdbsum/7pha PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pha ProSAT]</span></td></tr>
	[[~~Category~~: ~~Unreleased Structures~~]]		</table>
	[[~~Category~~: ~~Rappsilber~~, ~~J]]~~		__TOC__
	[[~~Category~~: ~~Xue, L]~~]		</StructureSection>
	[[Category: ~~Lenz, S~~]]		[[Category: Large Structures]]
	[[Category: ~~Mahamid, J~~]]		[[Category: Z-disk]]

OCA at 10:12, 13 October 2021

2021-10-13T10:12:22Z

← Older revision		Revision as of 10:12, 13 October 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Xue, L., Lenz, S., Rappsilber, J., Mahamid, J.		Authors: Xue, L., Lenz, S., Rappsilber, J., Mahamid, J.

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

2021-08-25T05:12:23Z

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

← Older revision	Revision as of 05:12, 25 August 2021
(No difference)

OCA: New page: '''Unreleased structure''' The entry 7pha is ON HOLD Authors: Xue, L., Lenz, S., Rappsilber, J., Mahamid, J. Description: 70S ribosome with EF-Tu-tRNA and P-site tRNA in chloramphenico...

2021-08-25T05:12:22Z

New page: '''Unreleased structure''' The entry 7pha is ON HOLD Authors: Xue, L., Lenz, S., Rappsilber, J., Mahamid, J. Description: 70S ribosome with EF-Tu-tRNA and P-site tRNA in chloramphenico...

New page

'''Unreleased structure'''

The entry 7pha is ON HOLD

Authors: Xue, L., Lenz, S., Rappsilber, J., Mahamid, J.

Description: 70S ribosome with EF-Tu-tRNA and P-site tRNA in chloramphenicol-treated Mycoplasma pneumoniae cells
[[Category: Unreleased Structures]]
[[Category: Rappsilber, J]]
[[Category: Xue, L]]
[[Category: Lenz, S]]
[[Category: Mahamid, J]]