5te3: Difference between revisions

Latest revision as of 12:58, 4 October 2023

Crystal structure of Bos taurus opsin at 2.7 Angstrom

Structural highlights

5te3 is a 1 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 2.7Å
Ligands:	BMA, BOG, MAN, NAG, PLM, SO4
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]

Publication Abstract from PubMed

Vertebrate rhodopsin (Rh) contains 11-cis-retinal as a chromophore to convert light energy into visual signals. On absorption of light, 11-cis-retinal is isomerized to all-trans-retinal, constituting a one-way reaction that activates transducin (Gt) followed by chromophore release. Here we report that bovine Rh, regenerated instead with a six-carbon-ring retinal chromophore featuring a C11=C12 double bond locked in its cis conformation (Rh6mr), employs an atypical isomerization mechanism by converting 11-cis to an 11,13-dicis configuration for prolonged Gt activation. Time-dependent UV-vis spectroscopy, HPLC, and molecular mechanics analyses revealed an atypical thermal reisomerization of the 11,13-dicis to the 11-cis configuration on a slow timescale, which enables Rh6mr to function in a photocyclic manner similar to that of microbial Rhs. With this photocyclic behavior, Rh6mr repeatedly recruits and activates Gt in response to light stimuli, making it an excellent candidate for optogenetic tools based on retinal analog-bound vertebrate Rhs. Overall, these comprehensive structure-function studies unveil a unique photocyclic mechanism of Rh activation by an 11-cis-to-11,13-dicis isomerization.

Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism.,Gulati S, Jastrzebska B, Banerjee S, Placeres AL, Miszta P, Gao S, Gunderson K, Tochtrop GP, Filipek S, Katayama K, Kiser PD, Mogi M, Stewart PL, Palczewski K Proc Natl Acad Sci U S A. 2017 Mar 13. pii: 201617446. doi:, 10.1073/pnas.1617446114. PMID:28289214^[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
↑ Gulati S, Jastrzebska B, Banerjee S, Placeres AL, Miszta P, Gao S, Gunderson K, Tochtrop GP, Filipek S, Katayama K, Kiser PD, Mogi M, Stewart PL, Palczewski K. Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism. Proc Natl Acad Sci U S A. 2017 Mar 13. pii: 201617446. doi:, 10.1073/pnas.1617446114. PMID:28289214 doi:https://dx.doi.org/10.1073/pnas.1617446114

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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

[2] 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

[3] Gulati S, Jastrzebska B, Banerjee S, Placeres AL, Miszta P, Gao S, Gunderson K, Tochtrop GP, Filipek S, Katayama K, Kiser PD, Mogi M, Stewart PL, Palczewski K. Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism. Proc Natl Acad Sci U S A. 2017 Mar 13. pii: 201617446. doi:, 10.1073/pnas.1617446114. PMID:28289214 doi:https://dx.doi.org/10.1073/pnas.1617446114

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
 ==Crystal structure of Bos taurus opsin at 2.7 Angstrom==
-<StructureSection load='5te3' size='340' side='right' caption='[[5te3]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='5te3' size='340' side='right'caption='[[5te3]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5te3]] is a 1 chain structure with sequence 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=5TE3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TE3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5te3]] is a 1 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=5TE3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TE3 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5te5|5te5]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PLM:PALMITIC+ACID'>PLM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5te3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5te3 OCA], [http://pdbe.org/5te3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5te3 RCSB], [http://www.ebi.ac.uk/pdbsum/5te3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5te3 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=5te3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5te3 OCA], [https://pdbe.org/5te3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5te3 RCSB], [https://www.ebi.ac.uk/pdbsum/5te3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5te3 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5te3" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Rhodopsin 3D structures|Rhodopsin 3D structures]]
 == References ==
 <references/>
@@ Line 24: / Line 27: @@
 </StructureSection>
 [[Category: Bos taurus]]
-[[Category: Gulati, S]]
+[[Category: Large Structures]]
-[[Category: Kiser, P D]]
+[[Category: Gulati S]]
-[[Category: Palczewski, K]]
+[[Category: Kiser PD]]
-[[Category: Signaling protein]]
+[[Category: Palczewski K]]

5te3: Difference between revisions

Latest revision as of 12:58, 4 October 2023

Crystal structure of Bos taurus opsin at 2.7 Angstrom

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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