5w0p - Revision history

OCA at 14:04, 4 October 2023

2023-10-04T14:04:22Z

←Older revision		Revision as of 14:04, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5w0p' size='340' side='right'caption='[[5w0p]], [[Resolution\|resolution]] 3.01Å' scene=''>		<StructureSection load='5w0p' size='340' side='right'caption='[[5w0p]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w0p]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0P OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5W0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w0p]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_RB55 Enterobacteria phage RB55], [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5W0P FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=NAG:N~~-~~ACETYL-D-GLUCOSAMINE'>NAG</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.013Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~SEP~~:~~PHOSPHOSERINE~~'>~~SEP~~</scene>, <scene name='pdbligand=~~TPO~~:~~PHOSPHOTHREONINE~~'>~~TPO~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[4zwj\|4zwj]]</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=5w0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0p OCA], [https://pdbe.org/5w0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5w0p RCSB], [https://www.ebi.ac.uk/pdbsum/5w0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0p ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</~~b></td><td class="sblockDat">Sag ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5w0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0p OCA], [~~http~~://pdbe.org/5w0p PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5w0p RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5w0p PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0p ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/OPSD_HUMAN OPSD_HUMAN] Retinitis punctata albescens;Congenital stationary night blindness;Retinitis pigmentosa. The disease is caused by variants affecting the gene represented in this entry. The disease is caused by variants affecting the gene represented in this entry.
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/~~A0A097J792_BPT4 A0A097J792_BPT4]~~] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.[~~HAMAP-Rule~~:~~MF_04110~~]	+	[https://www.uniprot.org/uniprot/OPSD_HUMAN OPSD_HUMAN] Photoreceptor required for image-forming vision at low light intensity (PubMed:8107847, PubMed:7846071). Required for photoreceptor cell viability after birth (PubMed:2215617, PubMed:12566452). Light-induced isomerization of the chromophore 11-cis-retinal to all-trans-retinal triggers a conformational change that activates signaling via G-proteins (PubMed:8107847, PubMed:28524165, PubMed:26200343, PubMed:28753425). Subsequent receptor phosphorylation mediates displacement of the bound G-protein alpha subunit by the arrestin SAG and terminates signaling (PubMed:28524165, PubMed:26200343).<ref>PMID:12566452</ref> <ref>PMID:2215617</ref> <ref>PMID:26200343</ref> <ref>PMID:28753425</ref> <ref>PMID:7846071</ref> <ref>PMID:8107847</ref> <ref>PMID:28524165</ref> [https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref> [https://www.uniprot.org/uniprot/ARRS_MOUSE ARRS_MOUSE] Binds to photoactivated, phosphorylated RHO and terminates RHO signaling via G-proteins by competing with G-proteins for the same binding site on RHO (PubMed:9333241, PubMed:16421323). May play a role in preventing light-dependent degeneration of retinal photoreceptor cells (PubMed:16421323).<ref>PMID:16421323</ref> <ref>PMID:9333241</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Enterobacteria phage RB55]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lysozyme~~]]	+	[[Category: Mus musculus]]
-	[[Category: Barty, A]]	+	[[Category: Barty A]]
-	[[Category: Chapman~~, H N~~]]	+	[[Category: Chapman HN]]
-	[[Category: Cherezov, V]]	+	[[Category: Cherezov V]]
-	[[Category: Dror~~, R O]]~~	+	[[Category: Dror RO]]
-	~~[[Category: Eps, N Van~~]]	+	[[Category: Ernst OP]]
-	[[Category: Ernst~~, O P~~]]	+	[[Category: Gao X]]
-	[[Category: Gao, X]]	+	[[Category: Goswami D]]
-	[[Category: Goswami, D]]	+	[[Category: Griffin PR]]
-	[[Category: Griffin~~, P R~~]]	+	[[Category: Gurevich VV]]
-	[[Category: Gurevich~~, V V~~]]	+	[[Category: He Y]]
-	[[Category: He, Y]]	+	[[Category: Hubbell WL]]
-	[[Category: Hubbell~~, W L~~]]	+	[[Category: Kang Y]]
-	[[Category: Kang, Y]]	+	[[Category: Latorraca NR]]
-	[[Category: Latorraca~~, N R~~]]	+	[[Category: Melcher K]]
-	[[Category: Melcher, K]]	+	[[Category: Pal K]]
-	[[Category: Pal, K]]	+	[[Category: Stevens RC]]
-	[[Category: Stevens~~, R C~~]]	+	[[Category: Van Eps N]]
-	[[Category: ~~Waal, P W.de~~]]	+	[[Category: White TA]]
-	[[Category: White~~, T A~~]]	+	[[Category: Xu HE]]
-	[[Category: Xu~~, H E~~]]	+	[[Category: Yin Y]]
-	[[Category: Yin, Y]]	+	[[Category: Zhou XE]]
-	[[Category: Zhou~~, X E~~]]	+	[[Category: De Waal PW]]
-	[[Category: ~~Arrestin]]~~	+
-	~~[[Category: Gpcr]]~~	+
-	~~[[Category: Grk]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Phosphorylation code]]~~	+
-	~~[[Category: Rhodopsin]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 17:27, 11 December 2019

2019-12-11T17:27:10Z

←Older revision		Revision as of 17:27, 11 December 2019
Line 1:		Line 1:

	==Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser==		==Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser==
-	<StructureSection load='5w0p' size='340' side='right' caption='[[5w0p]], [[Resolution\|resolution]] 3.01Å' scene=''>	+	<StructureSection load='5w0p' size='340' side='right'caption='[[5w0p]], [[Resolution\|resolution]] 3.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5w0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W0P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5w0p]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W0P FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zwj\|4zwj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zwj\|4zwj]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Sag ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5w0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0p OCA], [http://pdbe.org/5w0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w0p RCSB], [http://www.ebi.ac.uk/pdbsum/5w0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0p ProSAT]</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=5w0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0p OCA], [http://pdbe.org/5w0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w0p RCSB], [http://www.ebi.ac.uk/pdbsum/5w0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0p ProSAT]</span></td></tr>
Line 21:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5w0p" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5w0p" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Arrestin 3D structures\|Arrestin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Lysozyme]]		[[Category: Lysozyme]]
	[[Category: Barty, A]]		[[Category: Barty, A]]

OCA: Protected "5w0p" [edit=sysop:move=sysop]

2017-08-09T09:02:53Z

Protected "5w0p" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:02, 9 August 2017

OCA: New page: ==Crystal structure of rhodopsin bound to visual arrestin determined by X-ray free electron laser== == Structural highlights ==
<table><tr><td colspan='2'>[[5w0p]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5W0P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5W0P FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4zwj|4zwj]]</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lysozyme Lysozyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.17 3.2.1.17] </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=5w0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5w0p OCA], [http://pdbe.org/5w0p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5w0p RCSB], [http://www.ebi.ac.uk/pdbsum/5w0p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5w0p ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/A0A097J792_BPT4 A0A097J792_BPT4]] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.[HAMAP-Rule:MF_04110]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
G protein-coupled receptors (GPCRs) mediate diverse signaling in part through interaction with arrestins, whose binding promotes receptor internalization and signaling through G protein-independent pathways. High-affinity arrestin binding requires receptor phosphorylation, often at the receptor's C-terminal tail. Here, we report an X-ray free electron laser (XFEL) crystal structure of the rhodopsin-arrestin complex, in which the phosphorylated C terminus of rhodopsin forms an extended intermolecular beta sheet with the N-terminal beta strands of arrestin. Phosphorylation was detected at rhodopsin C-terminal tail residues T336 and S338. These two phospho-residues, together with E341, form an extensive network of electrostatic interactions with three positively charged pockets in arrestin in a mode that resembles binding of the phosphorylated vasopressin-2 receptor tail to beta-arrestin-1. Based on these observations, we derived and validated a set of phosphorylation codes that serve as a common mechanism for phosphorylation-dependent recruitment of arrestins by GPCRs.

Identification of Phosphorylation Codes for Arrestin Recruitment by G Protein-Coupled Receptors.,Zhou XE, He Y, de Waal PW, Gao X, Kang Y, Van Eps N, Yin Y, Pal K, Goswami D, White TA, Barty A, Latorraca NR, Chapman HN, Hubbell WL, Dror RO, Stevens RC, Cherezov V, Gurevich VV, Griffin PR, Ernst OP, Melcher K, Xu HE Cell. 2017 Jul 27;170(3):457-469.e13. doi: 10.1016/j.cell.2017.07.002. PMID:28753425<ref>PMID:28753425</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5w0p" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Lysozyme]]
[[Category: Barty, A]]
[[Category: Chapman, H N]]
[[Category: Cherezov, V]]
[[Category: Dror, R O]]
[[Category: Eps, N Van]]
[[Category: Ernst, O P]]
[[Category: Gao, X]]
[[Category: Goswami, D]]
[[Category: Griffin, P R]]
[[Category: Gurevich, V V]]
[[Category: He, Y]]
[[Category: Hubbell, W L]]
[[Category: Kang, Y]]
[[Category: Latorraca, N R]]
[[Category: Melcher, K]]
[[Category: Pal, K]]
[[Category: Stevens, R C]]
[[Category: Waal, P W.de]]
[[Category: White, T A]]
[[Category: Xu, H E]]
[[Category: Yin, Y]]
[[Category: Zhou, X E]]
[[Category: Arrestin]]
[[Category: Gpcr]]
[[Category: Grk]]
[[Category: Membrane protein]]
[[Category: Phosphorylation code]]
[[Category: Rhodopsin]]
[[Category: Signaling protein]]