4ZWJ

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

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: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8070800	3000473	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	G protein-coupled receptor-like	8070800	3000473	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Arrestin_C	e4zwjA2	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	e4zwjA4	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	e4zwjA1	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	e4zwjA3	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)
B	Arrestin_C	e4zwjB2	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	e4zwjB3	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	e4zwjB1	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)
C	Arrestin_C	e4zwjC2	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	e4zwjC3	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	e4zwjC1	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)
C	Phage_lysozyme_2	e4zwjC4	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)
D	Arrestin_C	e4zwjD4	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	e4zwjD3	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	e4zwjD1	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	e4zwjD2	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)	-	Family
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	Chimera protein of human Rhodopsin, mouse S-arrestin, and T4 Endolysin	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 signaling receptor binding G protein-coupled receptor binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process organic substance metabolic process aminoglycan metabolic process peptidoglycan metabolic process metabolic process macromolecule metabolic process organic substance catabolic 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 disruption of cellular anatomical structure in another organism exit from host cell viral process cytolysis in another organism cellular process 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 disruption of plasma membrane integrity in another organism 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 podosome assembly organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly cellular component organization cellular component biogenesis organelle organization cellular component assembly protein-containing complex assembly cellular component organization or biogenesis biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process gene expression macromolecule biosynthetic process multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis retina homeostasis photoreceptor cell maintenance detection of light stimulus detection of external stimulus detection of abiotic stimulus absorption of visible light detection of stimulus light absorption phototransduction regulation of biological process regulation of cellular process signaling biological regulation detection of visible light cell communication signal transduction phototransduction, visible light microtubule cytoskeleton organization microtubule-based process cytoskeleton organization sensory perception of light stimulus system process sensory perception nervous system process visual perception G protein-coupled receptor signaling pathway rhodopsin mediated signaling pathway 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 negative adaptation of signaling pathway import into cell receptor internalization negative regulation of signaling transport negative regulation of biological process desensitization of G protein-coupled receptor signaling pathway regulation of signal transduction negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication vesicle-mediated transport localization negative regulation of cellular process regulation of G protein-coupled receptor signaling pathway G protein-coupled receptor internalization regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction establishment of localization regulation of response to stimulus adaptation of signaling pathway regulation of cell communication receptor-mediated endocytosis endocytosis	host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity 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	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	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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	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, C, D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	Human rhodopsin with bound mouse visual arrestin

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.