6B73

Crystal Structure of a nanobody-stabilized active state of the kappa-opioid receptor

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
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: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d6b73c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d6b73c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d6b73d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d6b73d2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	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	8091210	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091210	3000473	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091210	3000473	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091210	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	e6b73A1	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	ECOD (1.6)
B	PF00001	e6b73B1	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	ECOD (1.6)
C	PF07686	e6b73C1	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	e6b73D1	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)

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	1.20.1070.10	Mainly Alpha	Up-down Bundle	Rhopdopsin 7-helix transmembrane proteins	Rhodopsin 7-helix transmembrane proteins	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV1	-	soluble cytochrome b562, kappa-type opioid receptor	SAbDab (2024-04-05)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07361	Cytochrome b562 (Cytochrom_B562)	Cytochrome b562	-	Family
A, B	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Soluble cytochrome b562, kappa-type opioid receptor	molecular transducer activity G protein-coupled opioid receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity amide binding binding neuropeptide binding peptide binding peptide receptor activity G protein-coupled peptide receptor activity dynorphin receptor activity protein binding receptor serine/threonine kinase binding molecular transducer activity G protein-coupled opioid receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity amide binding binding neuropeptide binding peptide binding peptide receptor activity G protein-coupled peptide receptor activity dynorphin receptor activity protein binding receptor serine/threonine kinase binding signaling receptor binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway behavior multicellular organismal process locomotory behavior cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cell communication G protein-coupled receptor signaling pathway cellular process signal transduction neuropeptide signaling pathway behavior multicellular organismal process locomotory behavior adult behavior response to organic substance response to organonitrogen compound response to oxygen-containing compound response to nitrogen compound response to alkaloid behavioral response to cocaine response to chemical response to organic cyclic compound response to cocaine response to hormone response to endogenous stimulus response to estrogen ovulation cycle rhythmic process estrous cycle reproductive process multicellular organismal reproductive process multicellular organism reproduction reproduction immune response immune system process homeostatic process response to monosaccharide response to carbohydrate carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus cellular response to organic substance cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis chemical homeostasis response to glucose glucose homeostasis G protein-coupled opioid receptor signaling pathway maternal behavior parental behavior reproductive behavior regulation of localization negative regulation of luteinizing hormone secretion system process regulation of system process negative regulation of biological process negative regulation of transport localization regulation of luteinizing hormone secretion negative regulation of secretion luteinizing hormone secretion negative regulation of hormone secretion negative regulation of secretion by cell regulation of biological quality regulation of hormone levels establishment of localization regulation of secretion endocrine hormone secretion negative regulation of gonadotropin secretion negative regulation of multicellular organismal process regulation of endocrine process regulation of hormone secretion gonadotropin secretion transport negative regulation of signaling hormone secretion negative regulation of cell communication secretion by cell regulation of secretion by cell signal release negative regulation of cellular process regulation of multicellular organismal process regulation of signaling secretion regulation of transport regulation of gonadotropin secretion cell-cell signaling export from cell endocrine process hormone transport regulation of cell communication eating behavior feeding behavior sensory perception nervous system process sensory perception of temperature stimulus biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide response to biotic stimulus cellular response to biotic stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway adenylate cyclase-inhibiting opioid receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway monoamine transport nitrogen compound transport regulation of catecholamine secretion positive regulation of biological process organic hydroxy compound transport positive regulation of secretion by cell dopamine transport positive regulation of amine transport catecholamine transport positive regulation of secretion positive regulation of cellular process organic substance transport positive regulation of catecholamine secretion dopamine secretion positive regulation of dopamine secretion catecholamine secretion amine transport positive regulation of transport regulation of amine transport regulation of dopamine secretion regulation of body fluid levels secretion by tissue digestive system process regulation of digestive system process body fluid secretion digestion saliva secretion regulation of saliva secretion response to alcohol response to ethanol phospholipase C-activating G protein-coupled receptor signaling pathway response to peptide hormone response to peptide response to insulin trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling chemical synaptic transmission positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction p38MAPK cascade intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade positive regulation of p38MAPK cascade regulation of response to stimulus regulation of p38MAPK cascade MAPK cascade positive regulation of signaling learning learning or memory cognition conditioned place preference associative learning regulation of eating behavior positive regulation of feeding behavior positive regulation of eating behavior regulation of behavior positive regulation of behavior positive regulation of multicellular organismal process regulation of feeding behavior sensory perception of pain defense response defense response to symbiont defense response to virus defense response to other organism response to stress response to virus positive regulation of cation transmembrane transport regulation of potassium ion transport monoatomic ion transmembrane transport potassium ion transmembrane transport regulation of monoatomic ion transmembrane transport metal ion transport monoatomic cation transmembrane transport positive regulation of monoatomic ion transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation transport regulation of metal ion transport regulation of monoatomic ion transport inorganic ion transmembrane transport regulation of potassium ion transmembrane transport inorganic cation transmembrane transport transmembrane transport positive regulation of potassium ion transport regulation of transmembrane transport positive regulation of potassium ion transmembrane transport potassium ion transport regulation of monoatomic cation transmembrane transport response to acrylamide	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane somatodendritic compartment cell body perikaryon neuronal cell body cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane somatodendritic compartment cell body perikaryon neuronal cell body intracellular anatomical structure cytoplasm cytosol presynapse presynaptic membrane cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular vesicle transport vesicle membrane endomembrane system bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane vesicle transport vesicle exocytic vesicle membrane cytoplasmic vesicle membrane secretory vesicle organelle membrane exocytic vesicle axon axon terminus distal axon neuron projection terminus periplasmic space
C, D	Nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001418	Opioid receptor	Family
A, B	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B	IPR000452	Kappa opioid receptor	Family
A, B	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, B	IPR010980	Cytochrome c/b562	Homologous Superfamily
A, B	IPR009155	Cytochrome b562	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P41145	Pain opiate dependence cocaine dependence substance withdrawal syndrome visual epilepsy cocaine abuse pilocytic astrocytoma depressive disorder medulloblastoma obesity disorder pain agnosia schizophrenia glioblastoma malignant ependymoma atypical teratoid rhabdoid tumor Pain opiate dependence cocaine dependence substance withdrawal syndrome visual epilepsy cocaine abuse pilocytic astrocytoma depressive disorder medulloblastoma obesity disorder pain agnosia schizophrenia glioblastoma malignant ependymoma atypical teratoid rhabdoid tumor large cell medulloblastoma malignant glioma astrocytic tumor oligodendroglioma

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	κ-opioid receptor, nanobody-stabilized active state

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.