5DYS

Crystal Structure of T94I rhodopsin mutant

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: PDBTM
Membrane Protein Annotation: MemProtMD
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5dysa_	Membrane and cell surface proteins and peptides	Class A G protein-coupled receptor (GPCR)-like	Class A G protein-coupled receptor (GPCR)-like	Rhodopsin-like	automated matches	Bovine (Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8042778	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)
A	7tm_1	e5dysA1	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)
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	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	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	Rhodopsin	opsin binding protein binding binding arrestin family protein binding G protein-coupled photoreceptor activity molecular transducer activity photoreceptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity vitamin binding retinal binding isoprenoid binding retinoid binding opsin binding protein binding binding arrestin family protein binding G protein-coupled photoreceptor activity molecular transducer activity photoreceptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity vitamin binding retinal binding isoprenoid binding retinoid binding lipid binding 11-cis retinal binding small molecule binding G-protein alpha-subunit binding GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding identical protein binding	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 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 process cellular response to stimulus response to light stimulus response to 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 response to external stimulus 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 metabolic process macromolecule metabolic 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	cellular anatomical structure membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle non-motile cilium 9+0 non-motile cilium cilium neuron projection photoreceptor disc membrane photoreceptor outer segment plasma membrane bounded cell projection cell projection cellular anatomical structure membrane cell-cell junction anchoring junction cell junction membrane-bounded organelle 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 organelle organelle membrane cell periphery protein-containing complex plasma membrane protein complex plasma membrane plasma membrane signaling receptor complex G protein-coupled receptor complex membrane protein complex receptor complex sperm midpiece 9+2 motile cilium sperm flagellum motile cilium photoreceptor inner segment membrane plasma membrane region photoreceptor inner segment ciliary membrane photoreceptor outer segment membrane bounding membrane of organelle cell projection membrane Golgi membrane intracellular anatomical structure Golgi apparatus intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasm outer 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	IPR027430	Visual pigments (opsins) retinal binding site	Binding Site
A	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A	IPR050125	G-protein coupled receptor opsins	Family
A	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A	IPR000732	Rhodopsin	Family
A	IPR019477	Rhodopsin, N-terminal	Domain
A	IPR001760	Opsin	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.