9FYR | pdb_00009fyr

Cryo-EM structure of native SV2A in complex with TeNT-Hc, Pro-Macrobody 5 and Levetiracetam

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	STI-like	8042036	3000715	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth D]	Heavy Chain	IGHV1	-	synaptic vesicle glycoprotein 2a	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	PF07951	Clostridium neurotoxin, C-terminal receptor binding (Toxin_R_bind_C)	Clostridium neurotoxin, C-terminal receptor binding	The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central tra ...	The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (Pfam:PF01742), the central translocation domains and two receptor binding domains [1]. This domain is the C-terminal receptor binding domain, which adopts a modified beta-trefoil fold with a six stranded beta-barrel and a beta-hairpin triplet capping the domain [1]. The first step in the intoxication process is a binding event between this domains and the pre-synaptic nerve ending [1].	Domain
A	PF07690	Major Facilitator Superfamily (MFS_1)	Major Facilitator Superfamily	-	Family
A	PF00083	Sugar (and other) transporter (Sugar_tr)	Sugar (and other) transporter	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D]	Pro-Macrobody 5,Maltose/maltodextrin-binding periplasmic protein,Maltose/maltodextrin-binding periplasmic protein	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope
B [auth C]	Tetanus toxin heavy chain	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity toxin activity cation binding macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity peptidase activity catalytic activity, acting on a protein metalloendopeptidase activity hydrolase activity metallopeptidase activity catalytic activity endopeptidase activity toxin activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host exocytosis symbiont-mediated perturbation of host process symbiont-mediated perturbation of host vesicle-mediated transport modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host neurotransmitter secretion proteolysis metabolic process cellular process primary metabolic process protein metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host exocytosis symbiont-mediated perturbation of host process symbiont-mediated perturbation of host vesicle-mediated transport modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host neurotransmitter secretion proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular region clathrin-coated vesicle coated vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane clathrin-coated endocytic vesicle coated vesicle membrane cytosol cell periphery plasma membrane
A	Synaptic vesicle glycoprotein 2A	transporter activity transmembrane transporter activity	localization transport neurotransmitter transport establishment of localization trans-synaptic signaling synaptic signaling regulation of biological process signaling anterograde trans-synaptic signaling biological regulation cell-cell signaling cellular process chemical synaptic transmission cell communication	membrane-bounded organelle intracellular anatomical structure synapse intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle presynapse cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane membrane-bounded organelle intracellular anatomical structure synapse intracellular vesicle transport vesicle membrane endomembrane system intracellular organelle presynapse cellular anatomical structure bounding membrane of organelle cytoplasmic vesicle vesicle membrane synaptic vesicle synaptic vesicle membrane cell junction vesicle transport vesicle membrane exocytic vesicle membrane intracellular membrane-bounded organelle cytoplasmic vesicle membrane organelle secretory vesicle cytoplasm organelle membrane exocytic vesicle cell projection neuron projection plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D]	IPR006061	Solute-binding family 1, conserved site	Conserved Site
C [auth D]	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
C [auth D]	IPR006059	Bacterial-type extracellular solute-binding protein	Family
B [auth C]	IPR000395	Botulinum/Tetanus toxin, catalytic chain	Domain
B [auth C]	IPR012928	Clostridium neurotoxin, receptor binding N-terminal	Domain
B [auth C]	IPR012500	Clostridium neurotoxin, translocation	Domain
B [auth C]	IPR011065	Kunitz inhibitor STI-like superfamily	Homologous Superfamily
B [auth C]	IPR013104	Clostridium neurotoxin, receptor-binding C-terminal	Domain
B [auth C]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B [auth C]	IPR036248	Clostridium neurotoxin, translocation domain	Homologous Superfamily
A	IPR022308	Synaptic vesicle protein SV2	Family
A	IPR055415	SV2A/B/C, luminal domain	Domain
A	IPR011701	Major facilitator superfamily	Family
A	IPR005828	Major facilitator, sugar transporter-like	Family
A	IPR036259	MFS transporter superfamily	Homologous Superfamily
A	IPR005829	Sugar transporter, conserved site	Conserved Site
A	IPR020846	Major facilitator superfamily domain	Domain

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, C [auth D]	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.