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4ww3

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Revision as of 20:59, 12 April 2023

Crystal structure of the lumi intermediate of squid rhodopsin

Structural highlights

4ww3 is a 2 chain structure with sequence from Todarodes pacificus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OPSD_TODPA Visual pigments such as rhodopsin and porphyropsin are light-absorbing molecules that mediate vision. Rhodopsin consists of an apoprotein, opsin, covalently linked to 11-cis-retinal. This receptor is coupled to the activation of phospholipase C. Porphyropsin consists of opsin covalently linked to 11-cis 3,4-didehydroretinal.

Publication Abstract from PubMed

Upon absorption of light, the retinal chromophore in rhodopsin isomerizes from the 11-cis to the trans configuration, initiating a photoreaction cycle. The primary photoreaction state, bathorhodopsin (BATHO), relaxes thermally through lumirhodopsin (LUMI) into a photoactive state, metarhodopsin (META), which stimulates the conjugated G-protein. Previous crystallographic studies of squid and bovine rhodopsins have shown that the structural change in the primary photoreaction of squid rhodopsin is considerably different from that observed in bovine rhodopsin. It would be expected that there is a fundamental difference in the subsequent thermal relaxation process between vertebrate and invertebrate rhodopsins. In this work, we performed crystallographic analyses of the LUMI state of squid rhodopsin using the P62 crystal. When the crystal was illuminated at 100 K with blue light, a half fraction of the protein was converted into BATHO. This reaction state relaxed into LUMI when the illuminated crystal was warmed in the dark to 170 K. It was found that, whereas trans retinal is largely twisted in BATHO, it takes on a more planar configuration in LUMI. This relaxation of retinal is accompanied by reorientation of the Schiff base NH bond, the hydrogen-bonding partner of which is switched to Asn185 in LUMI. Unlike bovine rhodopsin, the BATHO-to-LUMI transition in squid rhodopsin was accompanied by no significant change in the position/orientation of the beta-ionone ring of retinal.

Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin.,Murakami M, Kouyama T PLoS One. 2015 May 29;10(5):e0126970. doi: 10.1371/journal.pone.0126970., eCollection 2015. PMID:26024518^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Murakami M, Kouyama T. Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin. PLoS One. 2015 May 29;10(5):e0126970. doi: 10.1371/journal.pone.0126970., eCollection 2015. PMID:26024518 doi:http://dx.doi.org/10.1371/journal.pone.0126970

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ww3"

Categories: Large Structures | Todarodes pacificus | Kouyama T | Murakami M

@@ Line 3: / Line 3: @@
 <StructureSection load='4ww3' size='340' side='right'caption='[[4ww3]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ww3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Todarodes_pacificus Todarodes pacificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4WW3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ww3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Todarodes_pacificus Todarodes pacificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4WW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WW3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=PC1:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PC1</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TWT:DOCOSANE'>TWT</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=PC1:1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE'>PC1</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TWT:DOCOSANE'>TWT</scene></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=4ww3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ww3 OCA], [http://pdbe.org/4ww3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ww3 RCSB], [http://www.ebi.ac.uk/pdbsum/4ww3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ww3 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=4ww3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ww3 OCA], [https://pdbe.org/4ww3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ww3 RCSB], [https://www.ebi.ac.uk/pdbsum/4ww3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ww3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OPSD_TODPA OPSD_TODPA]] Visual pigments such as rhodopsin and porphyropsin are light-absorbing molecules that mediate vision. Rhodopsin consists of an apoprotein, opsin, covalently linked to 11-cis-retinal. This receptor is coupled to the activation of phospholipase C. Porphyropsin consists of opsin covalently linked to 11-cis 3,4-didehydroretinal.
+[https://www.uniprot.org/uniprot/OPSD_TODPA OPSD_TODPA] Visual pigments such as rhodopsin and porphyropsin are light-absorbing molecules that mediate vision. Rhodopsin consists of an apoprotein, opsin, covalently linked to 11-cis-retinal. This receptor is coupled to the activation of phospholipase C. Porphyropsin consists of opsin covalently linked to 11-cis 3,4-didehydroretinal.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 27: / Line 27: @@
 [[Category: Large Structures]]
 [[Category: Todarodes pacificus]]
-[[Category: Kouyama, T]]
+[[Category: Kouyama T]]
-[[Category: Murakami, M]]
+[[Category: Murakami M]]
-[[Category: 5-trisphosphate]]
-[[Category: Animal]]
-[[Category: Chemical]]
-[[Category: Decapodiforme]]
-[[Category: Inositol 1]]
-[[Category: Light]]
-[[Category: Model]]
-[[Category: Photochemistry]]
-[[Category: Protein conformation]]
-[[Category: Rhodopsin]]
-[[Category: Signaling protein]]

4ww3

From Proteopedia

Revision as of 20:59, 12 April 2023

Crystal structure of the lumi intermediate of squid rhodopsin

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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