3cap

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State

Structural highlights

3cap is a 2 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OPSD_BOVIN Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).^[1] ^[2]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

In the G-protein-coupled receptor (GPCR) rhodopsin, the inactivating ligand 11-cis-retinal is bound in the seven-transmembrane helix (TM) bundle and is cis/trans isomerized by light to form active metarhodopsin II. With metarhodopsin II decay, all-trans-retinal is released, and opsin is reloaded with new 11-cis-retinal. Here we present the crystal structure of ligand-free native opsin from bovine retinal rod cells at 2.9 angstrom (A) resolution. Compared to rhodopsin, opsin shows prominent structural changes in the conserved E(D)RY and NPxxY(x)(5,6)F regions and in TM5-TM7. At the cytoplasmic side, TM6 is tilted outwards by 6-7 A, whereas the helix structure of TM5 is more elongated and close to TM6. These structural changes, some of which were attributed to an active GPCR state, reorganize the empty retinal-binding pocket to disclose two openings that may serve the entry and exit of retinal. The opsin structure sheds new light on ligand binding to GPCRs and on GPCR activation.

Crystal structure of the ligand-free G-protein-coupled receptor opsin.,Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP Nature. 2008 Jul 10;454(7201):183-7. Epub 2008 Jun 18. PMID:18563085^[3]

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

References

↑ Nakamichi H, Okada T. Local peptide movement in the photoreaction intermediate of rhodopsin. Proc Natl Acad Sci U S A. 2006 Aug 22;103(34):12729-34. Epub 2006 Aug 14. PMID:16908857
↑ Salom D, Lodowski DT, Stenkamp RE, Le Trong I, Golczak M, Jastrzebska B, Harris T, Ballesteros JA, Palczewski K. Crystal structure of a photoactivated deprotonated intermediate of rhodopsin. Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16123-8. Epub 2006 Oct 23. PMID:17060607
↑ Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature. 2008 Jul 10;454(7201):183-7. Epub 2008 Jun 18. PMID:18563085 doi:10.1038/nature07063

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3cap"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3cap.png|left|200px]]
-<!--
+==Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State==
-The line below this paragraph, containing "STRUCTURE_3cap", creates the "Structure Box" on the page.
+<StructureSection load='3cap' size='340' side='right'caption='[[3cap]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3cap]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CAP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGL:B-2-OCTYLGLUCOSIDE'>BGL</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene></td></tr>
-{{STRUCTURE_3cap|  PDB=3cap  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cap OCA], [https://pdbe.org/3cap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cap RCSB], [https://www.ebi.ac.uk/pdbsum/3cap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cap ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OPSD_BOVIN OPSD_BOVIN] Photoreceptor required for image-forming vision at low light intensity. Required for photoreceptor cell viability after birth. Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal (By similarity).<ref>PMID:16908857</ref> <ref>PMID:17060607</ref>
+== 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/ca/3cap_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=3cap ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In the G-protein-coupled receptor (GPCR) rhodopsin, the inactivating ligand 11-cis-retinal is bound in the seven-transmembrane helix (TM) bundle and is cis/trans isomerized by light to form active metarhodopsin II. With metarhodopsin II decay, all-trans-retinal is released, and opsin is reloaded with new 11-cis-retinal. Here we present the crystal structure of ligand-free native opsin from bovine retinal rod cells at 2.9 angstrom (A) resolution. Compared to rhodopsin, opsin shows prominent structural changes in the conserved E(D)RY and NPxxY(x)(5,6)F regions and in TM5-TM7. At the cytoplasmic side, TM6 is tilted outwards by 6-7 A, whereas the helix structure of TM5 is more elongated and close to TM6. These structural changes, some of which were attributed to an active GPCR state, reorganize the empty retinal-binding pocket to disclose two openings that may serve the entry and exit of retinal. The opsin structure sheds new light on ligand binding to GPCRs and on GPCR activation.
-===Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State===
+Crystal structure of the ligand-free G-protein-coupled receptor opsin.,Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP Nature. 2008 Jul 10;454(7201):183-7. Epub 2008 Jun 18. PMID:18563085<ref>PMID:18563085</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3cap" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18563085}}, adds the Publication Abstract to the page
+*[[Rhodopsin|Rhodopsin]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18563085 is the PubMed ID number.
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_18563085}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-CAP is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CAP OCA].
-==Reference==
-<ref group="xtra">PMID:18563085</ref><references group="xtra"/>
 [[Category: Bos taurus]]
-[[Category: Choe, H W.]]
+[[Category: Large Structures]]
-[[Category: Ernst, O P.]]
+[[Category: Choe H-W]]
-[[Category: Hofmann, K P.]]
+[[Category: Ernst OP]]
-[[Category: Park, J H.]]
+[[Category: Hofmann KP]]
-[[Category: Scheerer, P.]]
+[[Category: Park JH]]
-[[Category: Acetylation]]
+[[Category: Scheerer P]]
-[[Category: Chromophore]]
-[[Category: G protein-coupled receptor]]
-[[Category: G-protein coupled receptor]]
-[[Category: Glycoprotein]]
-[[Category: Ligand-free state]]
-[[Category: Lipoprotein]]
-[[Category: Membrane protein]]
-[[Category: Opsin]]
-[[Category: Palmitate]]
-[[Category: Phosphoprotein]]
-[[Category: Photoreceptor]]
-[[Category: Photoreceptor protein]]
-[[Category: Retinal protein]]
-[[Category: Rhodopsin]]
-[[Category: Sensory transduction]]
-[[Category: Signaling protein]]
-[[Category: Transducer]]
-[[Category: Transmembrane]]
-[[Category: Vision]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:36:44 2009''

3cap

From Proteopedia

Current revision

Crystal Structure of Native Opsin: the G Protein-Coupled Receptor Rhodopsin in its Ligand-free State

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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