This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1f88

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

CRYSTAL STRUCTURE OF BOVINE RHODOPSIN

Structural highlights

1f88 is a 2 chain structure with sequence from Bos taurus. The March 2002 RCSB PDB Molecule of the Month feature on Bacteriorhodopsin by David S. Goodsell is 10.2210/rcsb_pdb/mom_2002_3. The October 2004 RCSB PDB Molecule of the Month feature on G Proteins by David S. Goodsell is 10.2210/rcsb_pdb/mom_2004_10. The June 2005 RCSB PDB Molecule of the Month feature on Carotenoid Oxygenase by David S. Goodsell is 10.2210/rcsb_pdb/mom_2005_6. The April 2008 RCSB PDB Molecule of the Month feature on Adrenergic Receptors by David S. Goodsell is 10.2210/rcsb_pdb/mom_2008_4. The March 2012 RCSB PDB Molecule of the Month feature on Rhodopsin by David Goodsell is 10.2210/rcsb_pdb/mom_2012_3. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1f88"

@@ Line 1: / Line 1: @@
-[[Image:1f88.gif|left|200px]]<br />
-<applet load="1f88" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1f88, resolution 2.8&Aring;" />
-'''CRYSTAL STRUCTURE OF BOVINE RHODOPSIN'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF BOVINE RHODOPSIN==
-Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled, receptors (GPCRs) respond to a variety of different external stimuli and, activate G proteins. GPCRs share many structural features, including a, bundle of seven transmembrane alpha helices connected by six loops of, varying lengths. We determined the structure of rhodopsin from diffraction, data extending to 2.8 angstroms resolution. The highly organized structure, in the extracellular region, including a conserved disulfide bridge, forms, a basis for the arrangement of the seven-helix transmembrane motif. The, ground-state chromophore, 11-cis-retinal, holds the transmembrane region, of the protein in the inactive conformation. Interactions of the, chromophore with a cluster of key residues determine the wavelength of the, maximum absorption. Changes in these interactions among rhodopsins, facilitate color discrimination. Identification of a set of residues that, mediate interactions between the transmembrane helices and the cytoplasmic, surface, where G-protein activation occurs, also suggests a possible, structural change upon photoactivation.
+<StructureSection load='1f88' size='340' side='right'caption='[[1f88]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1f88]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. The March 2002 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Bacteriorhodopsin''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2002_3 10.2210/rcsb_pdb/mom_2002_3]. The October 2004 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''G Proteins''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2004_10 10.2210/rcsb_pdb/mom_2004_10]. The June 2005 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Carotenoid Oxygenase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2005_6 10.2210/rcsb_pdb/mom_2005_6]. The April 2008 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Adrenergic Receptors''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2008_4 10.2210/rcsb_pdb/mom_2008_4]. The March 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Rhodopsin''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_3 10.2210/rcsb_pdb/mom_2012_3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F88 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F88 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1f88 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f88 OCA], [https://pdbe.org/1f88 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f88 RCSB], [https://www.ebi.ac.uk/pdbsum/1f88 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f88 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/f8/1f88_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/main_output.php?pdb_ID=1f88 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-F88 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with HG, ZN and RET as [http://en.wikipedia.org/wiki/ligands ligands]. The following pages contain interesting information on the relation of 1F88 with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb27_1.html Bacteriorhodopsin]], [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb58_1.html G Proteins]] and [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb66_1.html Carotenoid Oxygenase]]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1F88 OCA].
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
+== References ==
-==Reference==
+<references/>
-Crystal structure of rhodopsin: A G protein-coupled receptor., Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M, Science. 2000 Aug 4;289(5480):739-45. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10926528 10926528]
+__TOC__
+</StructureSection>
+[[Category: Adrenergic Receptors]]
 [[Category: Bacteriorhodopsin]]
+[[Category: Bos taurus]]
 [[Category: Carotenoid Oxygenase]]
 [[Category: G Proteins]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Miyano, M.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Okada, T.]]
+[[Category: Rhodopsin]]
-[[Category: Palczewski, K.]]
+[[Category: Miyano M]]
-[[Category: Stenkamp, R.E.]]
+[[Category: Okada T]]
-[[Category: HG]]
+[[Category: Palczewski K]]
-[[Category: RET]]
+[[Category: Stenkamp RE]]
-[[Category: ZN]]
-[[Category: g protein-coupled receptor]]
-[[Category: membrane protein]]
-[[Category: photoreceptor]]
-[[Category: retinal protein]]
-[[Category: visual pigment]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 08:59:53 2007''

1f88

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF BOVINE RHODOPSIN

Structural highlights

Function

Evolutionary Conservation

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox