4WW3

Crystal structure of the lumi intermediate of squid rhodopsin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091196	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091196	3000473	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	7tm_1	e4ww3B1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: 7tm_1	ECOD (1.6)
A	7tm_1	e4ww3A1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: 7tm_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)
A	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Rhodopsin	vitamin binding binding retinal binding isoprenoid binding retinoid binding lipid binding small molecule binding G protein-coupled photoreceptor activity molecular transducer activity photoreceptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity	cellular response to stimulus response to light stimulus response to stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular process cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus multicellular organismal process sensory perception of light stimulus system process sensory perception cellular response to stimulus response to light stimulus response to stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular process cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus multicellular organismal process sensory perception of light stimulus system process sensory perception nervous system process visual perception phototransduction detection of light stimulus detection of external stimulus regulation of biological process regulation of cellular process signaling biological regulation response to external stimulus detection of abiotic stimulus cell communication detection of stimulus signal transduction	cellular anatomical structure membrane cell periphery plasma membrane cell projection rhabdomere membrane rhabdomere plasma membrane region cell projection membrane plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006031	XYPPX repeat	Repeat
A, B	IPR027430	Visual pigments (opsins) retinal binding site	Binding Site
A, B	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B	IPR050125	G-protein coupled receptor opsins	Family
A, B	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, B	IPR001760	Opsin	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	G-protein coupled receptors, family A

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.