8DIT | pdb_00008dit

Cryo-EM structure of a HOPS core complex containing Vps33, Vps16, and Vps18

External Resource: Annotation

Domain Annotation: ECOD Classification
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	e8ditA1	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	e8ditA2	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	e8ditA3	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF04840	Vps16, C-terminal region (Vps16_C)	Vps16, C-terminal region	-	Repeat
B	PF04841	Vps16, N-terminal region (Vps16_N)	Vps16, N-terminal region	-	Repeat
C	PF05131	Pep3/Vps18/deep orange beta-propeller domain (Pep3_Vps18)	Pep3/Vps18/deep orange beta-propeller domain	-	Repeat
A	PF00995	Sec1 family (Sec1)	Sec1 family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Vacuolar protein sorting-associated protein 16	cytoskeletal protein binding actin binding protein binding binding	cellular localization establishment of protein localization nitrogen compound transport 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 cellular localization establishment of protein localization nitrogen compound transport 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
C	Vacuolar protein sorting-associated protein 18	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding protein-macromolecule adaptor activity molecular adaptor activity	cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport secretion cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport secretion export from cell membrane docking vesicle-mediated transport organelle localization by membrane tethering secretion by cell exocytosis organelle localization vesicle docking exocytic process vesicle docking involved in exocytosis organelle fusion cellular component organization organelle organization cellular component organization or biogenesis vacuole organization vesicle organization endosome organization endomembrane system organization	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	Vacuolar protein sorting-associated protein 33	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
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	IPR000547	Clathrin, heavy chain/VPS, 7-fold repeat	Repeat
C	IPR007810	Pep3/Vps18, beta-propeller domain	Domain
A	IPR027482	Sec1-like, domain 2	Homologous Superfamily
A	IPR043127	Sec1-like, domain 3a	Homologous Superfamily
A	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A	IPR001619	Sec1-like protein	Family
A	IPR043155	Vacuolar protein sorting-associated protein 33, domain 3b	Homologous Superfamily
A	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A	IPR043154	Sec1-like, domain 1	Homologous Superfamily
A	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.