3iyf - Revision history

OCA at 10:07, 21 February 2024

2024-02-21T10:07:47Z

←Older revision		Revision as of 10:07, 21 February 2024
Line 3:		Line 3:
	<SX load='3iyf' size='340' side='right' viewer='molstar' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>		<SX load='3iyf' size='340' side='right' viewer='molstar' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43000 Atcc 43000~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[3iye\|3iye]]</div></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]] 8Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">hsp60, MMP1515 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=39152 ATCC 43000])~~</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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [https://pdbe.org/3iyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [https://www.ebi.ac.uk/pdbsum/3iyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyf 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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [https://pdbe.org/3iyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [https://www.ebi.ac.uk/pdbsum/3iyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyf ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q877G8_METMI Q877G8_METMI]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iyf ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iyf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.
-
-	Mechanism of folding chamber closure in a group II chaperonin.,Zhang J, Baker ML, Schroder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W Nature. 2010 Jan 21;463(7279):379-83. PMID:20090755<ref>PMID:20090755</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3iyf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Chaperonin 3D structures\|Chaperonin 3D structures]]		*[[Chaperonin 3D structures\|Chaperonin 3D structures]]
	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]		*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</SX>		</SX>
-	[[Category: Atcc 43000]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Baker~~, M L~~]]	+	[[Category: Methanococcus maripaludis]]
-	[[Category: Chiu, W]]	+	[[Category: Baker ML]]
-	[[Category: Dougherty, M]]	+	[[Category: Chiu W]]
-	[[Category: Douglas~~, N R~~]]	+	[[Category: Dougherty M]]
-	[[Category: Frydman, J]]	+	[[Category: Douglas NR]]
-	[[Category: Fu~~, C J~~]]	+	[[Category: Frydman J]]
-	[[Category: Jakana, J]]	+	[[Category: Fu CJ]]
-	[[Category: Levitt, M]]	+	[[Category: Jakana J]]
-	[[Category: Ludtke~~, S J~~]]	+	[[Category: Levitt M]]
-	[[Category: Reissmann, S]]	+	[[Category: Ludtke SJ]]
-	[[Category: Schroeder, G]]	+	[[Category: Reissmann S]]
-	[[Category: Zhang, J]]	+	[[Category: Schroeder G]]
-	~~[[Category: Atp-binding]]~~	+	[[Category: Zhang J]]
-	~~[[Category: Chaperone]]~~	+
-	~~[[Category: Group ii chaperonin]]~~	+
-	~~[[Category: Methanococcus maripaludi]]~~	+
-	~~[[Category: Mm-cpn]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Protein folding]]~~	+
-	~~[[Category: Single particle reconstruction~~]]	+

OCA at 03:45, 21 April 2022

2022-04-21T03:45:23Z

←Older revision		Revision as of 03:45, 21 April 2022
Line 3:		Line 3:
	<SX load='3iyf' size='340' side='right' viewer='molstar' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>		<SX load='3iyf' size='340' side='right' viewer='molstar' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43000 Atcc 43000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3IYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43000 Atcc 43000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iye\|3iye]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3iye\|3iye]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 ATCC 43000])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 ATCC 43000])</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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [~~http~~://pdbe.org/3iyf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3iyf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyf 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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [https://pdbe.org/3iyf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [https://www.ebi.ac.uk/pdbsum/3iyf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 17:28, 10 April 2020

2020-04-10T17:28:10Z

←Older revision		Revision as of 17:28, 10 April 2020
Line 3:		Line 3:
	<SX load='3iyf' size='340' side='right' viewer='molstar' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>		<SX load='3iyf' size='340' side='right' viewer='molstar' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43000 Atcc 43000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43000 Atcc 43000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iye\|3iye]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iye\|3iye]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 ATCC 43000])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 ATCC 43000])</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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [http://pdbe.org/3iyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [http://www.ebi.ac.uk/pdbsum/3iyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyf 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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [http://pdbe.org/3iyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [http://www.ebi.ac.uk/pdbsum/3iyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 17:10, 6 March 2020

2020-03-06T17:10:32Z

←Older revision		Revision as of 17:10, 6 March 2020
Line 1:		Line 1:

	==Atomic Model of the Lidless Mm-cpn in the Open State==		==Atomic Model of the Lidless Mm-cpn in the Open State==
-	<~~StructureSection~~ load='3iyf' size='340' side='right' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>	+	<SX load='3iyf' size='340' side='right' viewer='molstar' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43000 Atcc 43000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYF FirstGlance]. <br>		<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43000 Atcc 43000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
Line 29:		Line 29:

	==See Also==		==See Also==
-	*[[Chaperonin\|Chaperonin]]	+	*[[Chaperonin 3D structures\|Chaperonin 3D structures]]
-	*[[Heat Shock ~~Proteins~~\|Heat Shock ~~Proteins~~]]	+	*[[Heat Shock Protein structures\|Heat Shock Protein structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Atcc 43000]]		[[Category: Atcc 43000]]
		+	[[Category: Large Structures]]
	[[Category: Baker, M L]]		[[Category: Baker, M L]]
	[[Category: Chiu, W]]		[[Category: Chiu, W]]

OCA at 08:01, 18 July 2018

2018-07-18T08:01:36Z

←Older revision		Revision as of 08:01, 18 July 2018
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/3iyf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/3iyf_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 16:24, 11 August 2016

2016-08-11T16:24:25Z

←Older revision		Revision as of 16:24, 11 August 2016
Line 1:		Line 1:
		+
	==Atomic Model of the Lidless Mm-cpn in the Open State==		==Atomic Model of the Lidless Mm-cpn in the Open State==
	<StructureSection load='3iyf' size='340' side='right' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>		<StructureSection load='3iyf' size='340' side='right' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanococcus_maripaludis Methanococcus maripaludis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43000 Atcc 43000]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iye\|3iye]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iye\|3iye]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 ~~Methanococcus maripaludis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 ATCC 43000])</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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [http://www.ebi.ac.uk/pdbsum/3iyf PDBsum]</span></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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [http://pdbe.org/3iyf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [http://www.ebi.ac.uk/pdbsum/3iyf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iyf ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3iyf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 26:
	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 3iyf" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanococcus maripaludis~~]]	+	[[Category: Atcc 43000]]
	[[Category: Baker, M L]]		[[Category: Baker, M L]]
	[[Category: Chiu, W]]		[[Category: Chiu, W]]

OCA at 10:34, 20 January 2015

2015-01-20T10:34:17Z

←Older revision		Revision as of 10:34, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYF FirstGlance]. <br>		<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iye\|3iye]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iye\|3iye]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 Methanococcus maripaludis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 Methanococcus maripaludis])</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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [http://www.ebi.ac.uk/pdbsum/3iyf PDBsum]</span></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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [http://www.ebi.ac.uk/pdbsum/3iyf PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Methanococcus maripaludis]]		[[Category: Methanococcus maripaludis]]
-	[[Category: Baker, M L.]]	+	[[Category: Baker, M L]]
-	[[Category: Chiu, W.]]	+	[[Category: Chiu, W]]
-	[[Category: Dougherty, M.]]	+	[[Category: Dougherty, M]]
-	[[Category: Douglas, N R.]]	+	[[Category: Douglas, N R]]
-	[[Category: Frydman, J.]]	+	[[Category: Frydman, J]]
-	[[Category: Fu, C J.]]	+	[[Category: Fu, C J]]
-	[[Category: Jakana, J.]]	+	[[Category: Jakana, J]]
-	[[Category: Levitt, M.]]	+	[[Category: Levitt, M]]
-	[[Category: Ludtke, S J.]]	+	[[Category: Ludtke, S J]]
-	[[Category: Reissmann, S.]]	+	[[Category: Reissmann, S]]
-	[[Category: Schroeder, G.]]	+	[[Category: Schroeder, G]]
-	[[Category: Zhang, J.]]	+	[[Category: Zhang, J]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Chaperone]]		[[Category: Chaperone]]

OCA at 12:29, 29 September 2014

2014-09-29T12:29:41Z

←Older revision		Revision as of 12:29, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3iyf.~~png~~\|~~left~~\|200px]]	+	==Atomic Model of the Lidless Mm-cpn in the Open State==
		+	<StructureSection load='3iyf' size='340' side='right' caption='[[3iyf]], [[Resolution\|resolution]] 8.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IYF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3iye\|3iye]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hsp60, MMP1515 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39152 Methanococcus maripaludis])</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=3iyf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iyf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3iyf RCSB], [http://www.ebi.ac.uk/pdbsum/3iyf PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/3iyf_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Group II chaperonins are essential mediators of cellular protein folding in eukaryotes and archaea. These oligomeric protein machines, approximately 1 megadalton, consist of two back-to-back rings encompassing a central cavity that accommodates polypeptide substrates. Chaperonin-mediated protein folding is critically dependent on the closure of a built-in lid, which is triggered by ATP hydrolysis. The structural rearrangements and molecular events leading to lid closure are still unknown. Here we report four single particle cryo-electron microscopy (cryo-EM) structures of Mm-cpn, an archaeal group II chaperonin, in the nucleotide-free (open) and nucleotide-induced (closed) states. The 4.3 A resolution of the closed conformation allowed building of the first ever atomic model directly from the single particle cryo-EM density map, in which we were able to visualize the nucleotide and more than 70% of the side chains. The model of the open conformation was obtained by using the deformable elastic network modelling with the 8 A resolution open-state cryo-EM density restraints. Together, the open and closed structures show how local conformational changes triggered by ATP hydrolysis lead to an alteration of intersubunit contacts within and across the rings, ultimately causing a rocking motion that closes the ring. Our analyses show that there is an intricate and unforeseen set of interactions controlling allosteric communication and inter-ring signalling, driving the conformational cycle of group II chaperonins. Beyond this, we anticipate that our methodology of combining single particle cryo-EM and computational modelling will become a powerful tool in the determination of atomic details involved in the dynamic processes of macromolecular machines in solution.

-	~~{{STRUCTURE_3iyf\| PDB=3iyf \| SCENE= }}~~	+	Mechanism of folding chamber closure in a group II chaperonin.,Zhang J, Baker ML, Schroder GF, Douglas NR, Reissmann S, Jakana J, Dougherty M, Fu CJ, Levitt M, Ludtke SJ, Frydman J, Chiu W Nature. 2010 Jan 21;463(7279):379-83. PMID:20090755<ref>PMID:20090755</ref>

-	~~===Atomic Model~~ of the ~~Lidless Mm-cpn in the Open State===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20090755}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3iyf]] is a 16 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA].~~	+

	==See Also==		==See Also==
	*[[Chaperonin\|Chaperonin]]		*[[Chaperonin\|Chaperonin]]
	*[[Heat Shock Proteins\|Heat Shock Proteins]]		*[[Heat Shock Proteins\|Heat Shock Proteins]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020090755<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Methanococcus maripaludis]]		[[Category: Methanococcus maripaludis]]
	[[Category: Baker, M L.]]		[[Category: Baker, M L.]]

OCA at 20:59, 20 October 2012

2012-10-20T20:59:40Z

←Older revision		Revision as of 20:59, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3iyf]] is a 16 chain structure ~~of [[Chaperonin]] and [[Heat Shock Proteins]]~~ with sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA].	+	[[3iyf]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA].

	==See Also==		==See Also==

OCA at 12:15, 27 July 2012

2012-07-27T12:15:37Z

←Older revision		Revision as of 12:15, 27 July 2012
Line 1:		Line 1:
	[[Image:3iyf.png\|left\|200px]]		[[Image:3iyf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3iyf", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3iyf\| PDB=3iyf \| SCENE= }}		{{STRUCTURE_3iyf\| PDB=3iyf \| SCENE= }}

	===Atomic Model of the Lidless Mm-cpn in the Open State===		===Atomic Model of the Lidless Mm-cpn in the Open State===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20090755}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20090755 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20090755}}		{{ABSTRACT_PUBMED_20090755}}

	==About this Structure==		==About this Structure==
-	[[3iyf]] is a 16 chain structure of [[Heat Shock Proteins]] with sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA].	+	[[3iyf]] is a 16 chain structure of [[Chaperonin]] and [[Heat Shock Proteins]] with sequence from [http://en.wikipedia.org/wiki/Methanococcus_maripaludis Methanococcus maripaludis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IYF OCA].

	==See Also==		==See Also==
-	*[[Heat Shock Proteins]]	+	*[[Chaperonin\|Chaperonin]]
		+	*[[Heat Shock Proteins\|Heat Shock Proteins]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20090755~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020090755</ref><references group="xtra"/>
	[[Category: Methanococcus maripaludis]]		[[Category: Methanococcus maripaludis]]
	[[Category: Baker, M L.]]		[[Category: Baker, M L.]]