3DYT | pdb_00003dyt

Crystal structure of Snx9PX-BAR (230-595), C2221

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	BAR/IMD domain-like	8053681	3000528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PX domain	8053687	3001006	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e3dytA5	A: DEATH domain	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: AsnC_trans_reg_3	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	CATH (4.3.0)
A	1.20.1270.60	Mainly Alpha	Up-down Bundle	Substrate Binding Domain Of Dnak	Chain:A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00787	PX domain (PX)	PX domain	PX domains bind to phosphoinositides.	Domain
A	PF10456	WASP-binding domain of Sorting nexin protein (BAR_3_WASP_bdg)	WASP-binding domain of Sorting nexin protein	The C-terminal region of the Sorting nexin group of proteins appears to carry a BAR-like (Bin/amphiphysin/Rvs) domain. This domain is very diverse and the similarities with other BAR domains are few. In the Sorting nexins it is associated with family ...	The C-terminal region of the Sorting nexin group of proteins appears to carry a BAR-like (Bin/amphiphysin/Rvs) domain. This domain is very diverse and the similarities with other BAR domains are few. In the Sorting nexins it is associated with family PX, Pfam:PF00787.13, and in combination with PX appears to be necessary to bind WASP along with p85 to form a multimeric signalling complex [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Sorting nexin-9	binding phospholipid binding lipid binding phosphatidylinositol binding identical protein binding protein binding protein homodimerization activity protein dimerization activity 1-phosphatidylinositol binding cell adhesion molecule binding cadherin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding binding phospholipid binding lipid binding phosphatidylinositol binding identical protein binding protein binding protein homodimerization activity protein dimerization activity 1-phosphatidylinositol binding cell adhesion molecule binding cadherin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding protein-containing complex binding Arp2/3 complex binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis membrane organization cytoskeleton-dependent cytokinesis cytokinesis cleavage furrow formation cytokinetic process membrane invagination cell cycle cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis membrane organization cytoskeleton-dependent cytokinesis cytokinesis cleavage furrow formation cytokinetic process membrane invagination cell cycle cell division plasma membrane invagination cell cycle process mitotic cell cycle process mitotic cytokinesis mitotic cell cycle localization import into cell transport endocytosis establishment of localization vesicle-mediated transport positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity regulation of localization cellular localization regulation of cellular process regulation of cellular component organization synaptic vesicle cycle regulation of synaptic vesicle recycling presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling regulation of synaptic vesicle endocytosis establishment of localization in cell regulation of endocytosis synaptic vesicle endocytosis regulation of biological process regulation of transport regulation of vesicle-mediated transport plasma membrane tubulation plasma membrane organization endomembrane system organization establishment of protein localization intracellular transport protein transport macromolecule localization intracellular protein localization intracellular protein transport endosomal transport positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process positive regulation of cellular component organization regulation of cellular component size positive regulation of biological process regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly positive regulation of protein polymerization actin filament-based process regulation of actin filament polymerization regulation of biological quality positive regulation of cellular process protein polymerization actin polymerization or depolymerization regulation of actin filament organization actin cytoskeleton organization actin filament polymerization positive regulation of cellular component biogenesis positive regulation of cytoskeleton organization regulation of actin polymerization or depolymerization actin filament organization regulation of cellular component biogenesis positive regulation of supramolecular fiber organization regulation of organelle organization organelle organization regulation of protein polymerization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization positive regulation of actin filament polymerization cytoskeleton organization regulation of anatomical structure size lipid tube assembly protein-lipid complex organization protein-lipid complex assembly regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity phosphorus metabolic process protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process positive regulation of kinase activity regulation of kinase activity macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process metabolic process macromolecule metabolic process regulation of metabolic process catabolic process positive regulation of membrane protein ectodomain proteolysis macromolecule catabolic process regulation of proteolysis proteolysis membrane protein proteolysis membrane protein ectodomain proteolysis regulation of membrane protein ectodomain proteolysis protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process positive regulation of proteolysis regulation of protein catabolic process receptor-mediated endocytosis	cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle cytoplasm cellular anatomical structure clathrin-coated pit membrane endomembrane system membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol cell periphery plasma membrane presynapse synapse cell junction cytoplasmic vesicle membrane vesicle membrane organelle membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network ruffle cell projection cell leading edge plasma membrane bounded cell projection cell cortex cuticular plate cortical cytoskeleton intracellular membraneless organelle actin cytoskeleton cytoskeleton membraneless organelle cortical actin cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001683	Phox homology	Domain
A	IPR036028	SH3-like domain superfamily	Homologous Superfamily
A	IPR027267	AH/BAR domain superfamily	Homologous Superfamily
A	IPR014536	Sorting nexin 9 family	Family
A	IPR019497	Sorting nexin protein, WASP-binding domain	Domain
A	IPR035558	SNX9, SH3 domain	Domain
A	IPR037425	Sorting nexin-9, BAR domain	Domain
A	IPR037426	Sorting nexin-9, PX domain	Domain
A	IPR036871	PX domain superfamily	Homologous Superfamily
A	IPR001452	SH3 domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9Y5X1	atopic eczema malignant pancreatic neoplasm ovarian cancer tuberculosis breast cancer MALT lymphoma pancreatic ductal adenocarcinoma ductal breast carcinoma in situ osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.