1bok - Revision history

OCA at 15:09, 2 June 2021

2021-06-02T15:09:07Z

←Older revision		Revision as of 15:09, 2 June 2021
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	<StructureSection load='1bok' size='340' side='right'caption='[[1bok]]' scene=''>		<StructureSection load='1bok' size='340' side='right'caption='[[1bok]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BOK FirstGlance]. <br>	+	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BOK FirstGlance]. <br>
-	</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=1bok FirstGlance], [~~http~~://www.ebi.ac.uk/pdbsum/1bok PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bok 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=1bok FirstGlance], [https://www.ebi.ac.uk/pdbsum/1bok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bok ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:28, 28 August 2019

2019-08-28T16:28:14Z

←Older revision		Revision as of 16:28, 28 August 2019
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	==BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL, THEORETICAL MODEL==		==BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL, THEORETICAL MODEL==
-	<StructureSection load='1bok' size='340' side='right' caption='[[1bok]]' scene=''>	+	<StructureSection load='1bok' size='340' side='right'caption='[[1bok]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BOK FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BOK FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Theoretical Model]]		[[Category: Theoretical Model]]
		+	[[Category: Large Structures]]
	[[Category: Lomize, A L]]		[[Category: Lomize, A L]]
	[[Category: Mosberg, H I]]		[[Category: Mosberg, H I]]
	[[Category: Pogozheva, I D]]		[[Category: Pogozheva, I D]]

OCA at 11:15, 22 November 2017

2017-11-22T11:15:41Z

←Older revision		Revision as of 11:15, 22 November 2017
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BOK FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BOK FirstGlance]. <br>
-	</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=1bok FirstGlance], [http://www.ebi.ac.uk/pdbsum/1bok PDBsum]</span></td></tr>	+	</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=1bok FirstGlance], [http://www.ebi.ac.uk/pdbsum/1bok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bok ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:44, 11 February 2016

2016-02-11T08:44:55Z

←Older revision		Revision as of 08:44, 11 February 2016
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		+	{{Theoretical_model}}
		+
	==BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL, THEORETICAL MODEL==		==BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL, THEORETICAL MODEL==
	<StructureSection load='1bok' size='340' side='right' caption='[[1bok]]' scene=''>		<StructureSection load='1bok' size='340' side='right' caption='[[1bok]]' scene=''>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Theoretical Model]]
	[[Category: Lomize, A L]]		[[Category: Lomize, A L]]
	[[Category: Mosberg, H I]]		[[Category: Mosberg, H I]]
	[[Category: Pogozheva, I D]]		[[Category: Pogozheva, I D]]

OCA at 17:01, 10 September 2015

2015-09-10T17:01:45Z

←Older revision		Revision as of 17:01, 10 September 2015
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	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 1bok" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:47, 22 December 2014

2014-12-22T09:47:21Z

←Older revision		Revision as of 09:47, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BOK FirstGlance]. <br>		<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BOK FirstGlance]. <br>
-	</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=1bok FirstGlance], [http://www.ebi.ac.uk/pdbsum/1bok PDBsum]</span></td></tr>	+	</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=1bok FirstGlance], [http://www.ebi.ac.uk/pdbsum/1bok PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 09:43, 13 August 2014

2014-08-13T09:43:52Z

←Older revision		Revision as of 09:43, 13 August 2014
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-	~~{{Theoretical_model}}~~	+	==BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL, THEORETICAL MODEL==
		+	<StructureSection load='1bok' size='340' side='right' caption='[[1bok]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BOK FirstGlance]. <br>
		+	</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=1bok FirstGlance], [http://www.ebi.ac.uk/pdbsum/1bok PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A 3D model of the transmembrane 7-alpha-bundle of rhodopsin-like G-protein-coupled receptors (GPCRs) was calculated using an iterative distance geometry refinement with an evolving system of hydrogen bonds, formed by intramembrane polar side chains in various proteins of the family and collectively applied as distance constraints. The alpha-bundle structure thus obtained provides H bonding of nearly all buried polar side chains simultaneously in the 410 GPCRs considered. Forty evolutionarily conserved GPCR residues form a single continuous domain, with an aliphatic "core" surrounded by six clusters of polar and aromatic side chains. The 7-alpha-bundle of a specific GPCR can be calculated using its own set of H bonds as distance constraints and the common "average" model to restrain positions of the helices. The bovine rhodopsin model thus determined is closely packed, but has a few small polar cavities, presumably filled by water, and has a binding pocket that is complementary to 11-cis (6-s-cis, 12-s-trans, C = N anti)-retinal or to all-trans-retinal, depending on conformations of the Lys296 and Trp265 side chains. A suggested mechanism of rhodopsin photoactivation, triggered by the cis-trans isomerization of retinal, involves rotations of Glu134, Tyr223, Trp265, Lys296, and Tyr306 side chains and rearrangement of their H bonds. The model is in agreement with published electron cryomicroscopy, mutagenesis, chemical modification, cross-linking, Fourier transform infrared spectroscopy, Raman spectroscopy, electron paramagnetic resonance spectroscopy, NMR, and optical spectroscopy data. The rhodopsin model and the published structure of bacteriorhodopsin have very similar retinal-binding pockets.

-	~~[[Image~~:~~1bok~~.~~png\|left\|200px]]~~	+	The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints.,Pogozheva ID, Lomize AL, Mosberg HI Biophys J. 1997 May;72(5):1963-85. PMID:9129801<ref>PMID:9129801</ref>

-	~~{{STRUCTURE_1bok\| PDB=1bok \| SCENE= }}~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~===BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL~~, ~~THEORETICAL MODEL===~~	+	== References ==
-		+	<references/>
-	~~{{ABSTRACT_PUBMED_9129801}}~~	+	__TOC__
-		+	</StructureSection>
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:009129801<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Lomize, A L]]		[[Category: Lomize, A L]]
	[[Category: Mosberg, H I]]		[[Category: Mosberg, H I]]
	[[Category: Pogozheva, I D]]		[[Category: Pogozheva, I D]]

OCA: Protected "1bok" [edit=sysop:move=sysop]

2012-10-21T09:37:07Z

Protected "1bok" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:37, 21 October 2012

OCA at 09:37, 21 October 2012

2012-10-21T09:37:02Z

←Older revision		Revision as of 09:37, 21 October 2012
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	{{Theoretical_model}}		{{Theoretical_model}}
-	~~{{Seed}}~~	+
	[[Image:1bok.png\|left\|200px]]		[[Image:1bok.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1bok", 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_1bok\| PDB=1bok \| SCENE= }}		{{STRUCTURE_1bok\| PDB=1bok \| SCENE= }}

	===BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL, THEORETICAL MODEL===		===BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL, THEORETICAL MODEL===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_9129801}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 9129801 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_9129801}}		{{ABSTRACT_PUBMED_9129801}}
-
-	==About this Structure==
-	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BOK OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~9129801~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:009129801</ref><references group="xtra"/>
	[[Category: Lomize, A L]]		[[Category: Lomize, A L]]
	[[Category: Mosberg, H I]]		[[Category: Mosberg, H I]]
	[[Category: Pogozheva, I D]]		[[Category: Pogozheva, I D]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 8 08:39:53 2010''

OCA at 05:39, 8 April 2010

2010-04-08T05:39:53Z

←Older revision		Revision as of 05:39, 8 April 2010
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-	~~'''Theoretical Model'''~~	+	{{Theoretical_model}}
		+	{{Seed}}
		+	[[Image:1bok.png\|left\|200px]]

-	The ~~entry 1BOK is a Theoretical Model titled 'BOVINE RHODOPSIN~~ (~~7-HELIX BUNDLE~~) ~~WITH 11-CIS RETINAL~~, ~~THEORETICAL MODEL'~~.	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_1bok", 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_1bok\| PDB=1bok \| SCENE= }}

-	~~[[Category:Theoretical Model]]~~	+	===BOVINE RHODOPSIN (7-HELIX BUNDLE) WITH 11-CIS RETINAL, THEORETICAL MODEL===


-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 30 09~~:49:~~00 2008~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_9129801}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 9129801 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_9129801}}
		+
		+	==About this Structure==
		+	Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BOK OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:9129801</ref><references group="xtra"/>
		+	[[Category: Lomize, A L]]
		+	[[Category: Mosberg, H I]]
		+	[[Category: Pogozheva, I D]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Apr 8 08:39:53 2010''