4P2A | pdb_00004p2a

Structure of mouse VPS26A bound to rat SNX27 PDZ domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d4p2ab1	All beta proteins	PDZ domain-like	PDZ domain-like	automated matches	automated matches	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d4p2ab2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	PDZ domain-like	8062276	3000388	SCOP2B (2022-06-29)
A	SCOP2 Family	Vps26-like	8044659	4004065	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arrestin/Vps26-like	8051910	3002071	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Arrestin/Vps26-like	8051911	3002071	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)
B	PDZ	e4p2aB1	A: beta barrels	X: PDZ domain (From Topology)	H: PDZ domain (From Topology)	T: PDZ domain	F: PDZ	ECOD (1.6)
A	Vps26_C	e4p2aA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Vps26_C	ECOD (1.6)
A	Vps26_N	e4p2aA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Vps26_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)
A	2.60.40.640	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain
A	PF03643	Vacuolar protein sorting-associated protein 26 (Vps26)	Vacuolar protein sorting-associated protein 26	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Sorting nexin-27	binding phospholipid binding lipid binding phosphatidylinositol binding ionotropic glutamate receptor binding protein binding signaling receptor binding glutamate receptor binding calcium-dependent protein binding phosphatidylinositol-3-phosphate binding phosphatidylinositol phosphate binding	positive regulation of AMPA glutamate receptor clustering regulation of localization regulation of postsynaptic membrane organization cellular localization positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization regulation of protein localization regulation of AMPA glutamate receptor clustering positive regulation of postsynaptic membrane organization positive regulation of biological process cellular component organization localization receptor clustering positive regulation of AMPA glutamate receptor clustering regulation of localization regulation of postsynaptic membrane organization cellular localization positive regulation of cellular component organization regulation of cellular process regulation of cellular component organization regulation of protein localization regulation of AMPA glutamate receptor clustering positive regulation of postsynaptic membrane organization positive regulation of biological process cellular component organization localization receptor clustering cellular component organization or biogenesis synapse organization intracellular protein localization regulation of receptor clustering postsynaptic membrane organization regulation of protein localization to membrane positive regulation of cellular process membrane organization regulation of biological process postsynapse organization positive regulation of receptor clustering AMPA glutamate receptor clustering biological regulation positive regulation of protein localization to membrane glutamate receptor clustering neurotransmitter-gated ion channel clustering localization within membrane protein localization to membrane regulation of glutamate receptor clustering cell junction organization regulation of cellular localization macromolecule localization positive regulation of protein localization cellular process regulation of postsynaptic membrane neurotransmitter receptor levels regulation of biological quality transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport establishment of localization in cell vacuolar transport protein localization to cell periphery establishment of protein localization nitrogen compound transport neurotransmitter receptor transport establishment of protein localization to membrane protein-containing complex localization vesicle-mediated transport to the plasma membrane neurotransmitter receptor transport to plasma membrane protein transport cellular response to endogenous stimulus cellular response to growth factor stimulus response to stimulus response to endogenous stimulus cellular response to nerve growth factor stimulus response to nerve growth factor response to growth factor cellular response to stimulus signaling signal transduction cell communication intracellular protein transport developmental process multicellular organismal process regulation of developmental process nervous system development developmental maturation synapse maturation regulation of synapse organization multicellular organism development regulation of synapse maturation anatomical structure development regulation of synapse structure or activity system development endosomal transport response to amine response to methamphetamine hydrochloride response to chemical response to nitrogen compound establishment of protein localization to plasma membrane endocytic recycling protein localization to plasma membrane endosome to plasma membrane protein transport	protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system intracellular anatomical structure WASH complex cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system intracellular anatomical structure WASH complex cytoplasm cytosol synapse cell junction glutamatergic synapse membrane-bounded organelle early endosome endosome intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle vesicle cell periphery immunological synapse plasma membrane postsynaptic recycling endosome recycling endosome postsynaptic endosome postsynapse postsynaptic early endosome endosome membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane Schaffer collateral - CA1 synapse
A	Vacuolar protein sorting-associated protein 26A	-	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 cytosolic transport retrograde transport, endosome to Golgi localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane membrane protein complex retromer complex retromer, cargo-selective complex cytosol endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane lytic vacuole vacuole lysosome tubular endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR037835	SNX27, RA domain	Domain
B	IPR001683	Phox homology	Domain
B	IPR000159	Ras-associating domain	Domain
B	IPR037827	SNX27, atypical FERM-like domain	Domain
B	IPR037833	SNX27, PX domain	Domain
B	IPR036034	PDZ superfamily	Homologous Superfamily
B	IPR036871	PX domain superfamily	Homologous Superfamily
B	IPR001478	PDZ domain	Domain
B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A	IPR028934	Vacuolar protein sorting protein 26 related	Family
A	IPR014752	Arrestin-like, C-terminal	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.