9nnz: Difference between revisions

Latest revision as of 07:12, 18 February 2026

Structure of rod opsin in complex with a megabody

Structural highlights

9nnz is a 2 chain structure with sequence from Bos taurus and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.94Å
Ligands:	BMA, NAG
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

Rhodopsin, the most intensively studied G protein-coupled receptor (GPCR), is activated by light-induced isomerization of its chromophore 11-cis-retinal. This study employed cryogenic electron microscopy (cryo-EM) to investigate rhodopsin structure using a megabody (Mb7) as a negative allosteric modulator. Three distinct cryo-EM structures were solved: ground-state rhodopsin, photoactivated rhodopsin, and apo-rhodopsin, all in complex with Mb7. Photoactivated rhodopsin and apo-rhodopsin, both in complex with Mb7, maintain a conformation remarkably similar to ground-state rhodopsin rather than adopting a Meta-II-like conformation. Structural elements, including the conserved residues of the NPxxY motif and the ionic lock, remain in positions corresponding to inactive rhodopsin. The megabody forms extensive interactions with rhodopsin's extracellular loop 2, N terminus, and glycans. The findings demonstrate that Mb7 stabilizes photoactivated rhodopsin in a Meta-I-like conformation, preventing progression to the active Meta-II state through specific immobilization of the extracellular domain. This work establishes a foundation for cryo-EM-guided discovery of ligands modulating rhodopsin.

Structural analysis of rhodopsin states in megabody complexes.,Salom D, Suder DS, Huang W, Wu A, Pardon E, Steyaert J, Kiser PD, Taylor DJ, Gonen S, Palczewski K Proc Natl Acad Sci U S A. 2026 Feb 10;123(6):e2532336123. doi: , 10.1073/pnas.2532336123. Epub 2026 Feb 6. PMID:41650224^[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
↑ Salom D, Suder DS, Huang W, Wu A, Pardon E, Steyaert J, Kiser PD, Taylor DJ, Gonen S, Palczewski K. Structural analysis of rhodopsin states in megabody complexes. Proc Natl Acad Sci U S A. 2026 Feb 10;123(6):e2532336123. PMID:41650224 doi:10.1073/pnas.2532336123

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] Salom D, Suder DS, Huang W, Wu A, Pardon E, Steyaert J, Kiser PD, Taylor DJ, Gonen S, Palczewski K. Structural analysis of rhodopsin states in megabody complexes. Proc Natl Acad Sci U S A. 2026 Feb 10;123(6):e2532336123. PMID:41650224 doi:10.1073/pnas.2532336123

[1]

[2]

[3]

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9nnz is ON HOLD  until Paper Publication
+==Structure of rod opsin in complex with a megabody==
+<StructureSection load='9nnz' size='340' side='right'caption='[[9nnz]], [[Resolution|resolution]] 3.94&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9nnz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9NNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9NNZ FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.94&#8491;</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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=9nnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9nnz OCA], [https://pdbe.org/9nnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9nnz RCSB], [https://www.ebi.ac.uk/pdbsum/9nnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9nnz 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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rhodopsin, the most intensively studied G protein-coupled receptor (GPCR), is activated by light-induced isomerization of its chromophore 11-cis-retinal. This study employed cryogenic electron microscopy (cryo-EM) to investigate rhodopsin structure using a megabody (Mb7) as a negative allosteric modulator. Three distinct cryo-EM structures were solved: ground-state rhodopsin, photoactivated rhodopsin, and apo-rhodopsin, all in complex with Mb7. Photoactivated rhodopsin and apo-rhodopsin, both in complex with Mb7, maintain a conformation remarkably similar to ground-state rhodopsin rather than adopting a Meta-II-like conformation. Structural elements, including the conserved residues of the NPxxY motif and the ionic lock, remain in positions corresponding to inactive rhodopsin. The megabody forms extensive interactions with rhodopsin's extracellular loop 2, N terminus, and glycans. The findings demonstrate that Mb7 stabilizes photoactivated rhodopsin in a Meta-I-like conformation, preventing progression to the active Meta-II state through specific immobilization of the extracellular domain. This work establishes a foundation for cryo-EM-guided discovery of ligands modulating rhodopsin.
-Authors: Suder, D.S., Gonen, S.
+Structural analysis of rhodopsin states in megabody complexes.,Salom D, Suder DS, Huang W, Wu A, Pardon E, Steyaert J, Kiser PD, Taylor DJ, Gonen S, Palczewski K Proc Natl Acad Sci U S A. 2026 Feb 10;123(6):e2532336123. doi: , 10.1073/pnas.2532336123. Epub 2026 Feb 6. PMID:41650224<ref>PMID:41650224</ref>
-Description: Structure of rod opsin in complex with a megabody
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Gonen, S]]
+<div class="pdbe-citations 9nnz" style="background-color:#fffaf0;"></div>
-[[Category: Suder, D.S]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bos taurus]]
+[[Category: Large Structures]]
+[[Category: Synthetic construct]]
+[[Category: Gonen S]]
+[[Category: Suder DS]]

9nnz: Difference between revisions

Latest revision as of 07:12, 18 February 2026

Structure of rod opsin in complex with a megabody

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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