6ZE9 | pdb_00006ze9

Non-native fold of the putative VPS39 zinc finger domain

External Resource: Annotation

Domain Annotation: ECOD Classification
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	C1-set	e6ze9C1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
B	C1-set	e6ze9B1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)
A	C1-set	e6ze9A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF10367	Vacuolar sorting protein 39 C-terminal zinc finger domain (zf-Vps39_C)	Vacuolar sorting protein 39 C-terminal zinc finger domain	This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex [2]. This is likely a zinc binding domain which shows some similarity to the RING fingers found at the C-terminus of pf Vps protein. Vps39 is thought ...	This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex [2]. This is likely a zinc binding domain which shows some similarity to the RING fingers found at the C-terminus of pf Vps protein. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [3]. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange [1]. This domain is involved in localisation and in mediating the interactions of Vps39 with Vps11 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Vam6/Vps39-like protein	molecular adaptor activity	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism cellular localization establishment of protein localization intracellular transport protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport endosome to lysosome transport lysosomal transport intercellular transport vacuolar transport late endosome to lysosome transport endosomal vesicle fusion regulation of cellular process regulation of cellular component organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly SNARE complex assembly regulation of biological process protein-containing complex organization biological regulation regulation of cellular component biogenesis regulation of SNARE complex assembly localization within membrane endocytic recycling endosomal transport vesicle-mediated transport to the plasma membrane	membrane coat protein-containing complex cellular anatomical structure intracellular anatomical structure AP-type membrane coat adaptor complex AP-3 adaptor complex membrane membrane protein complex cytoplasm coated membrane HOPS complex vesicle tethering complex vacuolar membrane membrane-bounded organelle membrane coat protein-containing complex cellular anatomical structure intracellular anatomical structure AP-type membrane coat adaptor complex AP-3 adaptor complex membrane membrane protein complex cytoplasm coated membrane HOPS complex vesicle tethering complex vacuolar membrane membrane-bounded organelle lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle organelle lysosomal membrane organelle membrane lysosome lysosomal HOPS complex vacuolar HOPS complex endosome membrane endosome intracellular vesicle endomembrane system cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle vesicle late endosome late endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR000547	Clathrin, heavy chain/VPS, 7-fold repeat	Repeat
A, B, C	IPR019452	Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated domain 1	Domain
A, B, C	IPR001180	Citron homology (CNH) domain	Domain
A, B, C	IPR032914	Vam6/VPS39/TRAP1 family	Family
A, B, C	IPR019453	Vacuolar sorting protein 39/Transforming growth factor beta receptor-associated zinc finger domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q96JC1	breast carcinoma schizophrenia breast cancer Mammary Neoplasms

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.