6FUF

Crystal structure of the rhodopsin-mini-Go complex

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
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6fufa_	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	e6fufA1	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	Gtr1_RagA_N	e6fufB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Gtr1_RagA_N	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)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

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)	-	Family
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
B	Guanine nucleotide-binding protein G(o) subunit alpha	enzyme regulator activity cyclase regulator activity molecular function regulator activity adenylate cyclase regulator activity mu-type opioid receptor binding protein binding binding signaling receptor binding G protein-coupled receptor binding opioid receptor binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding enzyme regulator activity cyclase regulator activity molecular function regulator activity adenylate cyclase regulator activity mu-type opioid receptor binding protein binding binding signaling receptor binding G protein-coupled receptor binding opioid receptor binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding peptide hormone receptor binding corticotropin-releasing hormone receptor binding corticotropin-releasing hormone receptor 1 binding hormone receptor binding neuropeptide receptor binding G protein-coupled serotonin receptor binding protein-containing complex binding G-protein beta/gamma-subunit complex binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity cation binding metal ion binding	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation adenylate cyclase-inhibiting serotonin receptor signaling pathway G protein-coupled serotonin receptor signaling pathway cell communication adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway cellular process signal transduction cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation adenylate cyclase-inhibiting serotonin receptor signaling pathway G protein-coupled serotonin receptor signaling pathway cell communication adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway cellular process signal transduction heart process multicellular organismal process system process regulation of heart contraction regulation of system process circulatory system process regulation of blood circulation regulation of multicellular organismal process heart contraction blood circulation behavior locomotory behavior transport secretion export from cell membrane docking establishment of localization vesicle-mediated transport localization organelle localization by membrane tethering secretion by cell exocytosis organelle localization vesicle docking exocytic process vesicle docking involved in exocytosis cellular response to nitrogen compound response to dopamine cellular response to dopamine response to monoamine response to catecholamine cellular response to catecholamine stimulus response to organic cyclic compound G protein-coupled dopamine receptor signaling pathway cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to monoamine stimulus response to chemical protein localization negative regulation of protein transport regulation of localization establishment of protein localization nitrogen compound transport negative regulation of biological process negative regulation of transport negative regulation of secretion cellular macromolecule localization negative regulation of hormone secretion negative regulation of secretion by cell regulation of biological quality regulation of peptide hormone secretion negative regulation of peptide hormone secretion regulation of hormone levels establishment of protein localization to extracellular region negative regulation of establishment of protein localization protein secretion regulation of protein secretion regulation of secretion negative regulation of protein secretion cellular localization regulation of hormone secretion regulation of protein localization regulation of peptide secretion negative regulation of signaling hormone secretion negative regulation of cell communication protein localization to extracellular region negative regulation of peptide secretion peptide secretion regulation of secretion by cell amide transport signal release negative regulation of cellular process negative regulation of protein localization regulation of signaling regulation of transport regulation of peptide transport regulation of establishment of protein localization cell-cell signaling regulation of protein transport peptide transport negative regulation of insulin secretion protein transport regulation of cellular localization regulation of insulin secretion peptide hormone secretion macromolecule localization hormone transport regulation of cell communication insulin secretion trans-synaptic signaling modulation of chemical synaptic transmission chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling postsynaptic modulation of chemical synaptic transmission muscle contraction muscle system process	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane protein-containing complex extrinsic component of plasma membrane catalytic complex plasma membrane protein complex cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane protein-containing complex extrinsic component of plasma membrane catalytic complex plasma membrane protein complex cytoplasmic side of membrane membrane protein complex heterotrimeric G-protein complex side of membrane cytoplasmic side of plasma membrane GTPase complex extrinsic component of membrane extrinsic component of cytoplasmic side of plasma membrane parallel fiber to Purkinje cell synapse excitatory synapse presynapse presynaptic membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm GABA-ergic synapse glutamatergic synapse cell body

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
B	IPR001019	Guanine nucleotide binding protein (G-protein), alpha subunit	Family
B	IPR011025	G protein alpha subunit, helical insertion	Homologous Superfamily
B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
B	IPR001408	G-protein alpha subunit, group I	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P09471	developmental and epileptic encephalopathy, 17 substance withdrawal syndrome epilepsy neurodevelopmental disorder with involuntary movements Neurodevelopmental Disorders ovarian cancer psoriasis astrocytic tumor developmental and epileptic encephalopathy facioscapulohumeral muscular dystrophy intellectual disability malignant colon neoplasm medulloblastoma oligodendroglioma pilocytic astrocytoma developmental and epileptic encephalopathy, 17 substance withdrawal syndrome epilepsy neurodevelopmental disorder with involuntary movements Neurodevelopmental Disorders ovarian cancer psoriasis astrocytic tumor developmental and epileptic encephalopathy facioscapulohumeral muscular dystrophy intellectual disability malignant colon neoplasm medulloblastoma oligodendroglioma pilocytic astrocytoma schizophrenia atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant ependymoma osteosarcoma primitive neuroectodermal tumor subependymal giant cell astrocytoma cerebrovascular disorder hepatocellular carcinoma lung carcinoma malignant glioma

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.