5BUZ | pdb_00005buz

Crystal Structure of a Complex Between the SNARE Vam3 and the HOPS Vps33-Vps16 subcomplex from Chaetomium thermophilum

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	SNARE fusion complex	8065296	3001549	SCOP2B (2022-06-29)
C	SCOP2 Family	SNARE fusion complex	8065295	4003812	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	SNARE fusion complex	8065296	3001549	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C		e5buzC01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F:	ECOD (v294.1)
E	PilN	e5buzE1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: PilN	ECOD (v294.1)
B	PilN	e5buzB1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Pseudouridine synthase	T: Pseudouridine synthase	F: PilN	ECOD (v294.1)
D	DHFR_1	e5buzD3	A: a/b three-layered sandwiches	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: DHFR_1	ECOD (v294.1)
D	Ribosomal_L30,Ribosomal_L30_N	e5buzD2	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Ribosomal_L30,Ribosomal_L30_N	ECOD (v294.1)
A	DHFR_1	e5buzA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: 26S proteasome subunit Rpn2 C-terminal domain	T: 26S proteasome subunit Rpn2 C-terminal domain	F: DHFR_1	ECOD (v294.1)
A	Ribosomal_L30,Ribosomal_L30_N	e5buzA3	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: Ribosomal_L30,Ribosomal_L30_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.2060	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 1	CATH (4.3.0)
D	3.40.50.1910	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 2	CATH (4.3.0)
D	3.90.830.10	Alpha Beta	Alpha-Beta Complex	Syntaxin Binding Protein 1	Chain A, domain 2	CATH (4.3.0)
D	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)
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
C, F	PF05739	SNARE domain (SNARE)	SNARE domain	Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE dom ...	Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex. It is composed of about 70 amino acids arranged in an alpha-helical structure [1].	Domain
B, E	PF04840	Vps16, C-terminal region (Vps16_C)	Vps16, C-terminal region	-	Repeat
A, D	PF00995	Sec1 family (Sec1)	Sec1 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F	SNAP receptor-like protein	protein binding binding SNARE binding fusogenic activity SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport post-Golgi vesicle-mediated transport vesicle-mediated transport cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport post-Golgi vesicle-mediated transport vesicle-mediated transport Golgi to vacuole transport intercellular transport vacuolar transport Golgi vesicle transport membrane organization membrane fusion organelle membrane fusion vesicle organization cellular component organization organelle fusion organelle organization cellular component organization or biogenesis vesicle fusion organelle localization by membrane tethering organelle localization vesicle docking membrane docking	cellular anatomical structure endomembrane system SNARE complex protein-containing complex intracellular anatomical structure membrane membrane protein complex cytoplasm
B, E	Putative vacuolar protein sorting-associated protein	cytoskeletal protein binding actin binding protein binding binding	cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization 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 cellular anatomical structure membrane membrane protein complex 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 cellular anatomical structure membrane membrane protein complex 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
A, D	SM (Sec1/Munc18-like) protein	catalytic activity ligase activity	localization transport cellular process establishment of localization vesicle-mediated transport	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR006012	Syntaxin/epimorphin, conserved site	Conserved Site
C, F	IPR000727	Target SNARE coiled-coil homology domain	Domain
C, F	IPR010989	SNARE	Homologous Superfamily
C, F	IPR006011	Syntaxin, N-terminal domain	Domain
C, F	IPR045242	Syntaxin	Family
B, E	IPR016534	Vacuolar protein sorting-associated protein 16	Family
B, E	IPR006925	Vps16, C-terminal	Domain
B, E	IPR038132	Vps16, C-terminal domain superfamily	Homologous Superfamily
B, E	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B, E	IPR006926	Vps16, N-terminal	Domain
A, D	IPR027482	Sec1-like, domain 2	Homologous Superfamily
A, D	IPR043127	Sec1-like, domain 3a	Homologous Superfamily
A, D	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, D	IPR001619	Sec1-like protein	Family
A, D	IPR043155	Vacuolar protein sorting-associated protein 33, domain 3b	Homologous Superfamily
A, D	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A, D	IPR043154	Sec1-like, domain 1	Homologous Superfamily
A, D	IPR036045	Sec1-like 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.