6DZZ

Cryo-EM Structure of the wild-type human serotonin transporter in complex with ibogaine and 15B8 Fab in the inward conformation

External Resource: Annotation

Domain Annotation: ECOD Classification
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
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SNF	e6dzzA1	A: alpha complex topology	X: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	H: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	T: Sodium:neurotransmitter symporter family (SNF)-like	F: SNF	ECOD (1.6)
B	V-set_8	e6dzzB1	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	V-set	e6dzzC1	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)

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	Fab 15B8	VH	Mus musculus (house mouse)	IGHV1-8201, IGHJ401	V-DOMAIN VH	IG	VH-V-KAPPA	IMGT (202415-0)
C	Fab 15B8	V-KAPPA	Mus musculus (house mouse)	IGKV3-201, IGKJ101	V-DOMAIN V-KAPPA	IG	VH-V-KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	sodium-dependent serotonin transporter	SAbDab (2024-04-19)
C	Light Chain	IGKV3	Kappa	sodium-dependent serotonin transporter	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00209	Sodium:neurotransmitter symporter family (SNF)	Sodium:neurotransmitter symporter family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Sodium-dependent serotonin transporter	monoatomic cation transmembrane transporter activity monoatomic cation channel activity passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding monoatomic cation transmembrane transporter activity monoatomic cation channel activity passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity transmembrane transporter activity cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding antiporter activity active transmembrane transporter activity secondary active transmembrane transporter activity cation binding cocaine binding ion binding organic cyclic compound binding heterocyclic compound binding small molecule binding alkali metal ion binding sodium ion binding metal ion binding nitric-oxide synthase binding enzyme binding identical protein binding monoamine transmembrane transporter activity serotonin binding amine binding syntaxin-1 binding SNARE binding syntaxin binding neurotransmitter transmembrane transporter activity cell adhesion molecule binding integrin binding signaling receptor binding monoatomic anion transmembrane transporter activity chloride transmembrane transporter activity solute:sodium symporter activity solute:monoatomic cation symporter activity organic hydroxy compound transmembrane transporter activity monoatomic anion:monoatomic cation symporter activity active monoatomic ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic anion:sodium symporter activity sodium ion transmembrane transporter activity serotonin:sodium:chloride symporter activity sodium:chloride symporter activity chloride:monoatomic cation symporter activity metal ion transmembrane transporter activity symporter activity inorganic anion transmembrane transporter activity	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation localization transport neurotransmitter transport establishment of localization response to stimulus response to chemical response to xenobiotic stimulus cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process monoamine transport import into cell cellular localization nitrogen compound transport organic substance transport serotonin uptake serotonin transport organic hydroxy compound transport establishment of localization in cell neurotransmitter uptake neurotransmitter reuptake regulation of tube diameter 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 regulation of growth regulation of developmental growth developmental growth growth organ growth negative regulation of organ growth negative regulation of developmental growth negative regulation of growth regulation of organ growth regulation of multicellular organismal process negative regulation of multicellular organismal process regulation of body fluid levels wound healing homotypic cell-cell adhesion cell activation hemostasis platelet aggregation blood coagulation cell adhesion cell-cell adhesion response to stress coagulation response to wounding platelet activation behavior learning or memory nervous system process cognition memory cellular response to stimulus response to organic substance response to lipid response to oxygen-containing compound cellular response to oxygen-containing compound response to retinoic acid cellular response to chemical stimulus cellular response to retinoic acid cellular response to lipid cellular response to organic substance response to toxic substance multi-multicellular organism process sperm ejaculation reproductive process multicellular organismal reproductive process mating behavior reproductive behavior insemination multi-organism reproductive process copulation regulation of thalamus size response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus regulation of localization signaling positive regulation of secretion by cell cell communication secretion by cell regulation of secretion by cell positive regulation of secretion signal release positive regulation of monoatomic ion transport monoatomic ion transport serotonin secretion positive regulation of serotonin secretion secretion regulation of transport regulation of monoatomic ion transport cell-cell signaling export from cell regulation of serotonin secretion regulation of secretion positive regulation of transport cellular response to nitrogen compound response to endogenous stimulus response to organonitrogen compound response to organophosphorus cellular response to organic cyclic compound cellular response to cGMP response to nitrogen compound response to cGMP response to purine-containing compound cellular response to endogenous stimulus cellular response to organonitrogen compound response to organic cyclic compound cell cycle regulation of cell cycle positive regulation of cell cycle negative regulation of neural precursor cell proliferation regulation of cerebellar granule cell precursor proliferation cell proliferation in external granule layer cell proliferation in hindbrain negative regulation of cerebellar granule cell precursor proliferation regulation of neural precursor cell proliferation head development negative regulation of cell population proliferation cell population proliferation animal organ development brain development central nervous system development regulation of cell population proliferation cerebellar granule cell precursor proliferation neural precursor cell proliferation hindbrain development rhythmic process circadian rhythm brain morphogenesis anatomical structure morphogenesis animal organ morphogenesis monoatomic ion transmembrane transport sodium ion transmembrane transport inorganic ion transmembrane transport metal ion transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport monoatomic cation transport sodium ion transport biological process involved in intraspecies interaction between organisms social behavior membrane depolarization regulation of membrane potential enteric nervous system development autonomic nervous system development negative regulation of signaling modulation of chemical synaptic transmission negative regulation of synaptic transmission, dopaminergic negative regulation of synaptic transmission negative regulation of cell communication synaptic signaling trans-synaptic signaling regulation of signaling regulation of synaptic transmission, dopaminergic chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication synaptic transmission, dopaminergic response to nutrient levels response to nutrient response to estradiol	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane serotonergic synapse presynapse presynaptic membrane cell projection cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane serotonergic synapse presynapse presynaptic membrane cell projection neuron projection plasma membrane bounded cell projection endosome membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane anchoring junction focal adhesion cell-substrate junction membrane microdomain membrane raft
B	15B8 antibody heavy chain	-	-	-
C	15B8 antibody light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000175	Sodium:neurotransmitter symporter	Family
A	IPR037272	Sodium:neurotransmitter symporter superfamily	Homologous Superfamily
A	IPR013086	Sodium:neurotransmitter symporter, serotonin, N-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P31645	obsessive-compulsive disorder major depressive disorder bipolar disorder schizophrenia Sudden infant death syndrome alcohol abuse avoidant personality disorder substance abuse narcissistic personality disorder autism cocaine abuse melancholia amphetamine abuse substance withdrawal syndrome mood disorder obsessive-compulsive disorder major depressive disorder bipolar disorder schizophrenia Sudden infant death syndrome alcohol abuse avoidant personality disorder substance abuse narcissistic personality disorder autism cocaine abuse melancholia amphetamine abuse substance withdrawal syndrome mood disorder Asperger syndrome fibromyalgia pulmonary hypertension cocaine dependence depressive disorder anxiety disorder endogenous depression generalized anxiety disorder panic disorder intellectual disability post-traumatic stress disorder bulimia nervosa lung adenocarcinoma Crohn disease alcohol dependence mixed anxiety and depressive disorder non-small cell lung carcinoma female stress incontinence personality disorder premature ejaculation lung cancer Sjogren syndrome drug dependence neurotic disorder dysthymic disorder obesity disorder osteosarcoma breast cancer lung carcinoma seasonal affective disorder conduct disorder social phobia substance dependence substance-related disorder attention deficit hyperactivity disorder, inattentive type

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Transmembrane	Alpha-helical polytopic	APC (Amino acid-Polyamine-organoCation) superfamily	Neurotransmitter: sodium symporter

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Neurotransmitter Sodium Symporter (NSS) Family	serotonin transporter in complex with paroxetine, ts2-inactive

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.