3AXA | pdb_00003axa

Crystal structure of afadin PDZ domain in complex with the C-terminal peptide from nectin-3

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d3axab_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	automated matches	mouse, mouse (Mus musculus ) [TaxId: 10090 ], mouse, mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3axaa_	All beta proteins	PDZ domain-like	PDZ domain-like	PDZ domain	automated matches	mouse, mouse (Mus musculus ) [TaxId: 10090 ], mouse, mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e3axaB1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: FtsJ	F:	ECOD (20:10:01)
A		e3axaA1	A: cradle loop barrel	X: RIFT-related	H: acid protease	T: Bse634I	F:	ECOD (20:10:01)

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	2.30.42.10	Mainly Beta	Roll	Pdz3 Domain	PDZ domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00595	PDZ domain (PDZ)	PDZ domain	PDZ domains are found in diverse signaling proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Afadin, Nectin-3	cell adhesion molecule binding protein binding binding cell adhesion mediator activity identical protein binding protein homodimerization activity protein dimerization activity small GTPase binding enzyme binding GTPase binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding cell adhesion molecule binding protein binding binding cell adhesion mediator activity identical protein binding protein homodimerization activity protein dimerization activity small GTPase binding enzyme binding GTPase binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding LIM domain binding protein domain specific binding	sexual reproduction reproductive process fertilization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction heterophilic cell-cell adhesion cell adhesion cell-cell adhesion cellular process sexual reproduction reproductive process fertilization biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction heterophilic cell-cell adhesion cell adhesion cell-cell adhesion cellular process multicellular organismal process regulation of cellular component organization regulation of cellular process cellular component organization cellular component biogenesis multicellular organism development cellular component assembly regulation of postsynapse assembly cell junction assembly anatomical structure development regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of synapse assembly regulation of biological quality system development developmental process regulation of biological process postsynapse organization postsynapse assembly biological regulation regulation of postsynapse organization nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly ear morphogenesis embryonic organ morphogenesis ear development sensory organ development animal organ development embryonic morphogenesis embryo development anatomical structure morphogenesis sensory organ morphogenesis inner ear development cochlea development inner ear morphogenesis cochlea morphogenesis animal organ morphogenesis embryonic organ development camera-type eye morphogenesis eye development visual system development retina development in camera-type eye retina morphogenesis in camera-type eye eye morphogenesis camera-type eye development sensory system development localization establishment of protein localization cellular localization establishment of protein localization to membrane establishment of protein localization to plasma membrane localization within membrane establishment of localization homophilic cell-cell adhesion macromolecule localization intracellular protein localization protein localization to cell junction lens morphogenesis in camera-type eye lens development in camera-type eye regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process epithelium development endothelial cell differentiation cellular developmental process endothelium development cell development tissue development epithelial cell differentiation endothelial cell development establishment of endothelial intestinal barrier epithelial cell development cell differentiation establishment of endothelial barrier protein-containing complex organization protein-containing complex assembly pore complex assembly bicellular tight junction assembly tight junction organization apical junction assembly tight junction assembly cell-cell junction assembly cell-cell junction organization head development forebrain development brain development pallium development cerebral cortex development central nervous system development telencephalon development negative regulation of locomotion regulation of cell motility negative regulation of biological process regulation of locomotion negative regulation of cellular process regulation of cell migration negative regulation of cell motility cell migration cell motility negative regulation of cell migration locomotion neuroepithelial cell differentiation columnar/cuboidal epithelial cell differentiation positive regulation of dendritic spine morphogenesis positive regulation of nervous system development cell projection organization positive regulation of dendritic spine development regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell morphogenesis regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis regulation of dendrite morphogenesis positive regulation of cell projection organization dendritic spine morphogenesis dendritic spine development dendritic spine organization regulation of cell projection organization positive regulation of cell development positive regulation of cell morphogenesis generation of neurons regulation of dendrite development positive regulation of multicellular organismal process regulation of neuron projection development positive regulation of cellular component organization regulation of developmental process plasma membrane bounded cell projection morphogenesis regulation of dendritic spine development cell morphogenesis regulation of nervous system development neurogenesis dendrite development positive regulation of neuron projection development positive regulation of cell differentiation positive regulation of neurogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development plasma membrane bounded cell projection organization dendrite morphogenesis positive regulation of dendrite morphogenesis cell morphogenesis involved in neuron differentiation neuron development regulation of dendritic spine morphogenesis neuron projection organization regulation of plasma membrane bounded cell projection organization regulation of growth developmental growth positive regulation of developmental growth developmental growth involved in morphogenesis positive regulation of dendrite extension cell growth dendrite extension neuron projection extension regulation of developmental growth developmental cell growth growth regulation of dendrite extension positive regulation of cell growth regulation of cell growth positive regulation of growth positive regulation of cell adhesion regulation of cell adhesion positive regulation of cell-cell adhesion positive regulation of cell-cell adhesion mediated by cadherin cell-cell adhesion mediated by cadherin regulation of cell-cell adhesion regulation of cell-cell adhesion mediated by cadherin dendrite arborization neuron projection arborization multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells brain morphogenesis oligodendrocyte progenitor proliferation cell population proliferation gliogenesis regulation of cell population proliferation neural precursor cell proliferation regulation of oligodendrocyte progenitor proliferation regulation of neural precursor cell proliferation adherens junction organization cell junction maintenance cellular component maintenance adherens junction maintenance cell-cell junction maintenance cellular response to stimulus response to stimulus signaling signal transduction cell communication organelle organization postsynaptic specialization organization glial cell differentiation radial glial cell differentiation regulation of localization regulation of protein localization positive regulation of cell communication regulation of postsynaptic membrane potential system process positive regulation of signal transduction modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential regulation of signal transduction chemical synaptic transmission, postsynaptic positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential mini excitatory postsynaptic potential trans-synaptic signaling regulation of signaling cell surface receptor signaling pathway nervous system process cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of mini excitatory postsynaptic potential positive regulation of mini excitatory postsynaptic potential regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region cell-cell junction anchoring junction somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection cell-cell contact zone apical junction complex adherens junction hippocampal mossy fiber to CA3 synapse axon apical part of cell membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck ribonucleoprotein granule intracellular organelle nuclear body nucleoplasm organelle lumen membraneless organelle supramolecular complex nuclear ribonucleoprotein granule nuclear lumen cytoplasm cytosol glutamatergic synapse protein-containing complex pore complex membrane protein complex presynaptic active zone membrane presynaptic membrane presynapse presynaptic active zone excitatory synapse tight junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR051427	Nectin and Nectin-like	Family
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR033319	Nectin-3, immunoglobulin variable domain 1	Domain
A, B	IPR013106	Immunoglobulin V-set domain	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR033320	Nectin-3/4, second Ig domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR013162	CD80-like, immunoglobulin C2-set	Domain
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR002710	Dilute domain	Domain
A, B	IPR028842	Afadin	Family
A, B	IPR037977	Afadin, cargo binding domain	Domain
A, B	IPR000159	Ras-associating domain	Domain
A, B	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A, B	IPR000253	Forkhead-associated (FHA) domain	Domain
A, B	IPR036034	PDZ superfamily	Homologous Superfamily
A, B	IPR001478	PDZ domain	Domain
A, B	IPR029071	Ubiquitin-like domain 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.