5TUD

Structural Insights into the Extracellular Recognition of the Human Serotonin 2B Receptor by an Antibody

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d5tudb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5tudb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d5tude2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d5tude1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d5tudc1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d5tudc2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d5tudf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d5tudf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	G protein-coupled receptor-like	8091214	3000473	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	G protein-coupled receptor-like	8091214	3000473	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytochromes	8057879	3001526	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytochromes	8057879	3001526	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091214	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091214	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)
D	7tm_1_2	e5tudD2	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_2	ECOD (1.6)
D	Cytochrom_B562_1	e5tudD1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Cytochromes (From Topology)	T: Cytochromes	F: Cytochrom_B562_1	ECOD (1.6)
A	7tm_1_2	e5tudA2	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_2	ECOD (1.6)
A	Cytochrom_B562_1	e5tudA1	A: alpha bundles	X: Four-helical up-and-down bundle	H: Cytochromes (From Topology)	T: Cytochromes	F: Cytochrom_B562_1	ECOD (1.6)
B	C1-set_4	e5tudB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
B	V-set	e5tudB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
E	C1-set_4	e5tudE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
E	V-set	e5tudE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
C	V-set_8	e5tudC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C	C1-set_1	e5tudC2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
F	V-set_8	e5tudF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F	C1-set_1	e5tudF2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, E	Anti-5-HT2B Fab	L-KAPPA	Mus musculus (house mouse)	IGKV4-5701, IGKJ501, IGKC*03	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)
C, F	Anti-5-HT2B Fab	VH-CH1	Mus musculus (house mouse)	IGHV1-5301, IGHJ201, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202446-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E	Light Chain	IGKV4	Kappa	5-hydroxytryptamine receptor 2b,soluble cytochrome b562chimera	SAbDab (2024-11-15)
C, F	Heavy Chain	IGHV1	-	5-hydroxytryptamine receptor 2b,soluble cytochrome b562chimera	SAbDab (2024-11-15)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF07361	Cytochrome b562 (Cytochrom_B562)	Cytochrome b562	-	Family
A, D	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, D	5-hydroxytryptamine receptor 2B,Soluble cytochrome b562 chimera	neurotransmitter receptor activity molecular transducer activity signaling receptor activity G protein-coupled amine receptor activity G protein-coupled serotonin receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity neurotransmitter receptor activity molecular transducer activity signaling receptor activity G protein-coupled amine receptor activity G protein-coupled serotonin receptor activity G protein-coupled receptor activity transmembrane signaling receptor activity GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity Gq/11-coupled serotonin receptor activity protein binding binding G-protein alpha-subunit binding cation binding ion binding serotonin binding organic cyclic compound binding amine binding heterocyclic compound binding small molecule binding tetrapyrrole binding heme binding electron transfer activity transition metal ion binding iron ion binding metal ion binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process neural crest cell differentiation cellular developmental process animal organ development mesenchyme development tissue development stem cell differentiation cell differentiation anatomical structure development cellular process mesenchymal cell differentiation response to stimulus response to chemical response to xenobiotic stimulus developmental process neural crest cell differentiation cellular developmental process animal organ development mesenchyme development tissue development stem cell differentiation cell differentiation anatomical structure development cellular process mesenchymal cell differentiation cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation phospholipase C-activating serotonin receptor signaling pathway G protein-coupled serotonin receptor signaling pathway cell communication phospholipase C-activating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction regulation of catalytic activity positive regulation of catalytic activity regulation of oxidoreductase activity positive regulation of oxidoreductase activity positive regulation of nitric-oxide synthase activity regulation of molecular function positive regulation of molecular function regulation of monooxygenase activity positive regulation of monooxygenase activity regulation of nitric-oxide synthase activity regulation of lipid metabolic process positive regulation of biological process glycerophospholipid metabolic process lipid biosynthetic process positive regulation of phosphate metabolic process regulation of primary metabolic process phospholipid metabolic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of lipid metabolic process positive regulation of phosphatidylinositol biosynthetic process phosphorus metabolic process positive regulation of cellular process regulation of phosphatidylinositol biosynthetic process regulation of biosynthetic process phosphatidylinositol metabolic process positive regulation of phosphorus metabolic process glycerophospholipid biosynthetic process positive regulation of phospholipid biosynthetic process regulation of phospholipid metabolic process primary metabolic process phospholipid biosynthetic process regulation of phospholipid biosynthetic process phosphatidylinositol biosynthetic process positive regulation of phospholipid metabolic process biosynthetic process positive regulation of lipid biosynthetic process glycerolipid biosynthetic process organophosphate metabolic process organophosphate biosynthetic process metabolic process regulation of phosphorus metabolic process glycerolipid metabolic process regulation of lipid biosynthetic process regulation of metabolic process lipid metabolic process regulation of tube diameter multicellular organismal process system process regulation of tube size circulatory system process vascular process in circulatory system blood vessel diameter maintenance regulation of biological quality vasoconstriction blood circulation regulation of anatomical structure size inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis positive regulation of cell division cell division regulation of cell division regulation of behavior behavior regulation of multicellular organismal process multicellular organism development anatomical structure morphogenesis embryonic morphogenesis embryo development heart development heart morphogenesis circulatory system development animal organ morphogenesis system development trans-synaptic signaling synaptic signaling anterograde trans-synaptic signaling cell-cell signaling chemical synaptic transmission phosphorylation cellular response to temperature stimulus response to abiotic stimulus response to temperature stimulus 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 G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger positive regulation of cell communication positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction positive regulation of signaling intestine smooth muscle contraction gastro-intestinal system smooth muscle contraction smooth muscle contraction phasic smooth muscle contraction muscle contraction muscle system process positive regulation of ERK1 and ERK2 cascade positive regulation of MAPK cascade regulation of MAPK cascade MAPK cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death cGMP-mediated signaling calcium-mediated signaling stem cell development neural crest cell development cell development mesenchymal cell migration ameboidal-type cell migration cell migration cell motility neural crest cell migration 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 serotonin 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 cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of phosphorylation regulation of transferase activity regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity positive regulation of macromolecule metabolic process protein modification process positive regulation of protein phosphorylation positive regulation of MAP kinase activity protein phosphorylation regulation of protein metabolic process positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity macromolecule modification macromolecule metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity positive regulation of transferase activity regulation of protein kinase activity regulation of macromolecule metabolic process regulation of phosphorylation regulation of localization cellular localization monoatomic ion transmembrane transport negative regulation of sequestering of calcium ion calcium ion transport metal ion transport maintenance of location in cell monoatomic cation transmembrane transport monoatomic ion transport monoatomic cation transport regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol sequestering of calcium ion inorganic ion transmembrane transport inorganic cation transmembrane transport maintenance of location transmembrane transport release of sequestered calcium ion into cytosol calcium ion transmembrane transport muscle hypertrophy cardiac muscle hypertrophy striated muscle hypertrophy positive regulation of macromolecule biosynthetic process cytokine production regulation of cytokine production gene expression macromolecule biosynthetic process regulation of gene expression positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production protein kinase C signaling endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation electron transport chain generation of precursor metabolites and energy	protein-containing complex G protein-coupled serotonin receptor complex receptor complex somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cell periphery plasma membrane protein-containing complex G protein-coupled serotonin receptor complex receptor complex somatodendritic compartment cell projection cellular anatomical structure dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm cell periphery plasma membrane membrane membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen synapse cell junction periplasmic space
B, E	Anti-5-HT2B Fab light chain	-	-	-
C, F	Anti-5-HT2B Fab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR002231	5-hydroxytryptamine receptor family	Family
A, D	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, D	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, D	IPR000482	5-Hydroxytryptamine 2B receptor	Family
A, D	IPR010980	Cytochrome c/b562	Homologous Superfamily
A, D	IPR009155	Cytochrome b562	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D	Pharos: P41595	congestive heart failure heart valve disease pulmonary hypertension Cardiomegaly hypertensive disorder psoriasis acromegaly amenorrhea invasive ductal breast carcinoma malignant mesothelioma pulmonary arterial hypertension adrenal cortex carcinoma migraine disorder osteosarcoma heart failure congestive heart failure heart valve disease pulmonary hypertension Cardiomegaly hypertensive disorder psoriasis acromegaly amenorrhea invasive ductal breast carcinoma malignant mesothelioma pulmonary arterial hypertension adrenal cortex carcinoma migraine disorder osteosarcoma heart failure major depressive disorder

Membrane Protein Annotation: OPM OPM Database Homepage

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

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.