4BX9 | pdb_00004bx9

Human Vps33A in complex with a fragment of human Vps16

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Vps16_C	e4bx9C1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Vps16_C	ECOD (1.6)
B	Sec1_3rd	e4bx9B2	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)
B	Sec1_2nd	e4bx9B4	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)
B	Sec1_1st	e4bx9B3	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)
A	Sec1_3rd	e4bx9A3	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	e4bx9A4	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	e4bx9A1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	1.10.150.780	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	3.40.50.2060	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 1	CATH (4.3.0)
B	3.40.50.1910	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Sec1/Munc18 (SM) protein, domain 2	CATH (4.3.0)
B	3.90.830.10	Alpha Beta	Alpha-Beta Complex	Syntaxin Binding Protein 1	Chain A, domain 2	CATH (4.3.0)
B	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
A, B	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	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 16 HOMOLOG	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding	cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization establishment of localization in cell cellular process vacuolar transport cellular component disassembly catabolic process protein-containing complex organization cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization establishment of localization in cell cellular process vacuolar transport cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism organelle fusion vacuole fusion organelle organization vacuole organization vacuole fusion, non-autophagic regulation of cellular process regulation of cellular component organization membrane fusion organelle membrane fusion cellular component biogenesis vesicle organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly SNARE complex assembly membrane organization regulation of biological process biological regulation regulation of cellular component biogenesis regulation of SNARE complex assembly vesicle fusion establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization intracellular protein transport endosomal transport endosomal vesicle fusion	membrane-bounded organelle protein-containing complex intracellular anatomical structure CORVET complex endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system vesicle tethering complex intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm membrane-bounded organelle protein-containing complex intracellular anatomical structure CORVET complex endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system vesicle tethering complex intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle clathrin-coated vesicle coated vesicle presynapse synapse cell junction endosome membrane membrane late endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane late endosome organelle membrane lytic vacuole vacuole lysosome early endosome autophagosome membrane protein complex HOPS complex vacuolar membrane lytic vacuole membrane lysosomal membrane recycling endosome somatodendritic compartment cell body neuronal cell body axon cell projection neuron projection plasma membrane bounded cell projection
A, B	VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 33A	-	cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization establishment of localization in cell cellular process vacuolar transport cellular component disassembly catabolic process protein-containing complex organization cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization establishment of localization in cell cellular process vacuolar transport cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism organelle localization lysosome localization vacuolar localization pigmentation regulation of biological process developmental pigmentation biological regulation regulation of developmental pigmentation regulation of pigmentation regulation of cellular process regulation of cellular component organization membrane fusion organelle membrane fusion cellular component biogenesis vesicle organization regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly SNARE complex assembly membrane organization regulation of cellular component biogenesis organelle fusion organelle organization regulation of SNARE complex assembly vesicle fusion establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization intracellular protein transport developmental process cellular developmental process hemopoiesis platelet morphogenesis cell development cell morphogenesis anatomical structure morphogenesis myeloid cell differentiation cell differentiation platelet formation anatomical structure development anatomical structure formation involved in morphogenesis vesicle localization pigment granule localization cellular pigmentation melanosome localization endosomal vesicle fusion vacuole organization lytic vacuole organization homeostatic process regulation of intracellular pH lysosome organization cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis regulation of biological quality monoatomic cation homeostasis regulation of lysosomal lumen pH regulation of cellular pH intracellular monoatomic ion homeostasis	membrane-bounded organelle protein-containing complex intracellular anatomical structure CORVET complex endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system vesicle tethering complex intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm membrane-bounded organelle protein-containing complex intracellular anatomical structure CORVET complex endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system vesicle tethering complex intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle clathrin-coated vesicle coated vesicle endosome membrane membrane late endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane late endosome organelle membrane lytic vacuole vacuole lysosome early endosome autophagosome membrane protein complex HOPS complex vacuolar membrane lytic vacuole membrane lysosomal membrane perinuclear region of cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR016534	Vacuolar protein sorting-associated protein 16	Family
C	IPR006925	Vps16, C-terminal	Domain
C	IPR038132	Vps16, C-terminal domain superfamily	Homologous Superfamily
C	IPR006926	Vps16, N-terminal	Domain
A, B	IPR043154	Sec1-like, domain 1	Homologous Superfamily
A, B	IPR036045	Sec1-like superfamily	Homologous Superfamily
A, B	IPR027482	Sec1-like, domain 2	Homologous Superfamily
A, B	IPR043155	Vacuolar protein sorting-associated protein 33, domain 3b	Homologous Superfamily
A, B	IPR043127	Sec1-like, domain 3a	Homologous Superfamily
A, B	IPR001619	Sec1-like protein	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: Q9H269	dystonic disorder osteosarcoma ovarian cancer
A, B	Pharos: Q96AX1	mucopolysaccharidosis-like syndrome with congenital heart defects and hematopoietic disorders mucopolysaccharidosis allergic rhinitis psoriasis inborn errors of metabolism lysosomal storage disease osteosarcoma

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.