5BV0

Crystal Structure of a Complex Between the SNARE Nyv1 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Sec1_3rd	e5bv0A2	A: alpha complex topology	X: alpha-helical domain in sec1/munc18-like (SM) proteins (From Topology)	H: alpha-helical domain in sec1/munc18-like (SM) proteins (From Topology)	T: alpha-helical domain in sec1/munc18-like (SM) proteins	F: Sec1_3rd	ECOD (1.6)
A	Sec1_2nd	e5bv0A4	A: a/b three-layered sandwiches	X: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	H: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	T: Rossmann-like domains in Sec1/munc18-like proteins	F: Sec1_2nd	ECOD (1.6)
A	Sec1_1st	e5bv0A3	A: a/b three-layered sandwiches	X: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	H: Rossmann-like domains in Sec1/munc18-like proteins (From Topology)	T: Rossmann-like domains in Sec1/munc18-like proteins	F: Sec1_1st	ECOD (1.6)
B	Vps16_C	e5bv0B1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Vps16_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2060	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 1	CATH (4.3.0)
A	3.40.50.1910	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 2	CATH (4.3.0)
A	3.90.830.10	Alpha Beta	Alpha-Beta Complex	Syntaxin Binding Protein 1	Chain A, domain 2	CATH (4.3.0)
A	1.25.40.850	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Sec1/Munc18 (SM) protein, domain 3b	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00995	Sec1 family (Sec1)	Sec1 family	-	Family
C	PF00957	Synaptobrevin (Synaptobrevin)	Synaptobrevin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	SM (Sec1/Munc18-like) protein	catalytic activity ligase activity	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport vesicle-mediated transport	membrane-bounded organelle storage vacuole intracellular anatomical structure lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle organelle cytoplasm protein-containing complex CORVET complex endosome membrane-bounded organelle storage vacuole intracellular anatomical structure lytic vacuole vacuole cellular anatomical entity intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle organelle cytoplasm protein-containing complex CORVET complex endosome intracellular vesicle endomembrane system vesicle tethering complex cytoplasmic vesicle vesicle
B	Vps16	cytoskeletal protein binding actin binding protein binding binding	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport vesicle-mediated transport endosomal transport organelle fusion cellular component organization vacuole fusion organelle organization vacuole organization vacuole fusion, non-autophagic cellular component organization or biogenesis	protein-containing complex membrane membrane protein complex cellular anatomical entity HOPS complex vesicle tethering complex membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle protein-containing complex membrane membrane protein complex cellular anatomical entity HOPS complex vesicle tethering complex membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle
C	SNARE domain	protein binding binding SNARE binding SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	membrane organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization cellular process cellular component organization or biogenesis vesicle fusion membrane organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization cellular process cellular component organization or biogenesis vesicle fusion secretion by cell exocytosis secretion export from cell	SNARE complex protein-containing complex intracellular anatomical structure membrane membrane protein complex cellular anatomical entity cytoplasm membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000608	Ubiquitin-conjugating enzyme E2	Domain
A	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A	IPR043154	Sec1-like, domain 1	Homologous Superfamily
A	IPR036045	Sec1-like superfamily	Homologous Superfamily
A	IPR027482	Sec1-like, domain 2	Homologous Superfamily
A	IPR043127	Sec1-like, domain 3a	Homologous Superfamily
A	IPR001619	Sec1-like protein	Family
A	IPR043155	Vacuolar protein sorting-associated protein 33, domain 3b	Homologous Superfamily
B	IPR016534	Vacuolar protein sorting-associated protein 16	Family
B	IPR006925	Vps16, C-terminal	Domain
B	IPR038132	Vps16, C-terminal domain superfamily	Homologous Superfamily
B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B	IPR006926	Vps16, N-terminal	Domain
C	IPR010908	Longin domain	Domain
C	IPR001388	Synaptobrevin-like	Family
C	IPR042855	v-SNARE, coiled-coil homology domain	Domain
C	IPR051097	Synaptobrevin-like vesicular transport protein	Family
C	IPR011012	Longin-like domain superfamily	Homologous Superfamily

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.