5DGY | pdb_00005dgy

Crystal structure of rhodopsin bound to visual arrestin

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
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)
D	SCOP2B Superfamily	G protein-coupled receptor-like	8070800	3000473	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	G protein-coupled receptor-like	8070800	3000473	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8070800	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8070800	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)
D	Arrestin_C	e5dgyD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arrestin_C	ECOD (1.6)
D	Arrestin_N	e5dgyD4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arrestin_N	ECOD (1.6)
D	7tm_1	e5dgyD2	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)
D	Phage_lysozyme_2	e5dgyD3	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)
C	Arrestin_C	e5dgyC3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arrestin_C	ECOD (1.6)
C	Arrestin_N	e5dgyC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arrestin_N	ECOD (1.6)
C	7tm_1	e5dgyC4	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)
B	Arrestin_C	e5dgyB3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arrestin_C	ECOD (1.6)
B	Arrestin_N	e5dgyB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arrestin_N	ECOD (1.6)
B	7tm_1	e5dgyB1	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	Arrestin_C	e5dgyA4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arrestin_C	ECOD (1.6)
A	Arrestin_N	e5dgyA3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Arrestin_N	ECOD (1.6)
A	7tm_1	e5dgyA2	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	Phage_lysozyme_2	e5dgyA1	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00339	Arrestin (or S-antigen), N-terminal domain (Arrestin_N)	Arrestin (or S-antigen), N-terminal domain	Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain.	Domain
A, B, C, D	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
A, B, C, D	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GC ...	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1].	Domain
A, B, C, D	PF02752	Arrestin (or S-antigen), C-terminal domain (Arrestin_C)	Arrestin (or S-antigen), C-terminal domain	Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain.	Domain
A, B, C, D	PF10413	Amino terminal of the G-protein receptor rhodopsin (Rhodopsin_N)	Amino terminal of the G-protein receptor rhodopsin	Rhodopsin is the archetypal G-protein-coupled receptor. Such receptors participate in virtually all physiological processes, as signalling molecules. They utilise heterotrimeric guanosine triphosphate (GTP)-binding proteins to transduce extracellular ...	Rhodopsin is the archetypal G-protein-coupled receptor. Such receptors participate in virtually all physiological processes, as signalling molecules. They utilise heterotrimeric guanosine triphosphate (GTP)-binding proteins to transduce extracellular signals to intracellular events. Rhodopsin is important because of the pivotal role it plays in visual signal transduction. Rhodopsin is a dimeric transmembrane protein and its intradiskal surface consists of this amino terminal domain and three loops connecting six of the seven transmembrane helices. The N-terminus is a compact domain of alpha-helical regions with breaks and bends at proline residues outside the membrane [1]. The transmembrane part of rhodopsin is represented by 7tm_1 (Pfam:PF00001). The N-terminal domain is extracellular is and is necessary for successful dimerisation and molecular stability [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Endolysin,Rhodopsin,S-arrestin	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity G protein-coupled photoreceptor activity photoreceptor activity vitamin binding binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity G protein-coupled photoreceptor activity photoreceptor activity vitamin binding binding retinal binding isoprenoid binding retinoid binding lipid binding 11-cis retinal binding small molecule binding cation binding ion binding metal ion binding cytoskeletal protein binding spectrin binding protein-containing complex binding protein binding opsin binding phosphoprotein binding	defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process defense response to bacterium biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process cellular process macromolecule metabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis exit from host cell viral process cytolysis in another organism viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process multicellular organismal process rod bipolar cell differentiation cellular developmental process sensory organ development retina development in camera-type eye visual system development neural retina development neurogenesis multicellular organism development eye morphogenesis neuron differentiation cell differentiation anatomical structure development animal organ morphogenesis sensory system development system development developmental process camera-type eye morphogenesis eye development animal organ development nervous system development retinal bipolar neuron differentiation glutamatergic neuron differentiation generation of neurons retina morphogenesis in camera-type eye anatomical structure morphogenesis sensory organ morphogenesis camera-type eye development cellular response to stimulus response to light stimulus cellular response to light stimulus response to radiation response to abiotic stimulus cellular response to radiation cellular response to abiotic stimulus cellular response to environmental stimulus regulation of cellular process signaling detection of abiotic stimulus cell communication signal transduction detection of light stimulus phototransduction detection of external stimulus regulation of biological process biological regulation detection of visible light detection of stimulus G protein-coupled receptor signaling pathway G protein-coupled opsin signaling pathway phototransduction, visible light response to light intensity podosome assembly organelle assembly protein-containing complex organization membraneless organelle assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis biosynthetic process gene expression macromolecule biosynthetic process multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis retina homeostasis photoreceptor cell maintenance absorption of visible light light absorption microtubule cytoskeleton organization microtubule-based process cytoskeleton organization sensory perception of light stimulus system process sensory perception nervous system process visual perception thermoception sensory perception of temperature stimulus detection of temperature stimulus involved in sensory perception response to temperature stimulus detection of temperature stimulus involved in thermoception detection of temperature stimulus detection of stimulus involved in sensory perception taxis thermotaxis locomotion	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle intracellular anatomical structure intracellular vesicle host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle Golgi-associated vesicle membrane organelle cytoplasm Golgi-associated vesicle vesicle organelle membrane photoreceptor inner segment non-motile cilium 9+0 non-motile cilium cilium neuron projection photoreceptor disc membrane photoreceptor outer segment plasma membrane bounded cell projection cell projection photoreceptor cell cilium cell periphery plasma membrane sperm midpiece 9+2 motile cilium sperm flagellum motile cilium photoreceptor inner segment membrane plasma membrane region ciliary membrane cell projection membrane photoreceptor outer segment membrane Golgi apparatus endomembrane system Golgi membrane sperm head sperm head plasma membrane sperm plasma membrane rod photoreceptor outer segment

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR052619	Bacteriophage lysozyme-like	Family
A, B, C, D	IPR001165	T4-type lysozyme	Family
A, B, C, D	IPR034690	Endolysin T4 type	Family
A, B, C, D	IPR002196	Glycoside hydrolase, family 24	Family
A, B, C, D	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A, B, C, D	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR027430	Visual pigments (opsins) retinal binding site	Binding Site
A, B, C, D	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B, C, D	IPR050125	G-protein coupled receptor opsins	Family
A, B, C, D	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, B, C, D	IPR000732	Rhodopsin	Family
A, B, C, D	IPR019477	Rhodopsin, N-terminal	Domain
A, B, C, D	IPR001760	Opsin	Family
A, B, C, D	IPR017864	Arrestin, conserved site	Conserved Site
A, B, C, D	IPR000698	Arrestin	Family
A, B, C, D	IPR011021	Arrestin-like, N-terminal	Domain
A, B, C, D	IPR011022	Arrestin C-terminal-like domain	Domain
A, B, C, D	IPR014753	Arrestin, N-terminal	Homologous Superfamily
A, B, C, D	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, B, C, D	IPR014752	Arrestin-like, C-terminal	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P08100	retinitis pigmentosa retinal degeneration congenital stationary night blindness congenital stationary night blindness autosomal dominant 1 retinitis pigmentosa 4 fundus albipunctatus night blindness retinitis pigmentosa 2 X-Linked Csnb blindness (disorder) inherited retinal dystrophy osteosarcoma cone-rod dystrophy congenital stationary night blindness 1B Leber congenital amaurosis retinitis pigmentosa retinal degeneration congenital stationary night blindness congenital stationary night blindness autosomal dominant 1 retinitis pigmentosa 4 fundus albipunctatus night blindness retinitis pigmentosa 2 X-Linked Csnb blindness (disorder) inherited retinal dystrophy osteosarcoma cone-rod dystrophy congenital stationary night blindness 1B Leber congenital amaurosis psoriasis retinitis pigmentosa 1 cone-rod synaptic disorder, congenital nonprogressive congenital stationary night blindness 2A hereditary night blindness