8FD1

Crystal structure of photoactivated rhodopsin in complex with a nanobody

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
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)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8042778	3000473	SCOP2B (2022-06-29)
B	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	PF00001,PF10413	e8fd1A1	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: PF00001,PF10413	ECOD (1.6)
B	PF00001,PF10413	e8fd1B1	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: PF00001,PF10413	ECOD (1.6)
C	PF07686	e8fd1C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07686	e8fd1D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV3	-	rhodopsin	SAbDab (2024-05-03)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	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 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 organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance 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 detection of light stimulus detection of external stimulus response to 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	membrane cellular anatomical entity 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 membrane cellular anatomical entity 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
C, D	Nanobody Nb2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR027430	Visual pigments (opsins) retinal binding site	Binding Site
A, B	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, B	IPR000732	Rhodopsin	Family
A, B	IPR019477	Rhodopsin, N-terminal	Domain
A, B	IPR001760	Opsin	Family

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 R01GM133198.