5Y04 | pdb_00005y04

Crystal Structure of the complex between the vinculin D1 domain and alphaE-catenin

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)
A	d5y04a1	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin-like	alpha-catenin/vinculin	Vinculin	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	Vinculin	e5y04B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: beta-helix of amnionless (AMN) extracellular domain	T: beta-helix of amnionless (AMN) extracellular domain	F: Vinculin	ECOD (v294.1)
A	V-set	e5y04A1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.230	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Alpha-catenin/vinculin-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01044	Vinculin family (Vinculin)	Vinculin family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Catenin alpha-1	gamma-catenin binding protein binding binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding vinculin binding cell adhesion molecule binding cadherin binding structural molecule activity beta-catenin binding identical protein binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development cellular response to stimulus negative regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cellular process response to stimulus signal transduction in absence of ligand negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand signal transduction regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process biological regulation cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication cellular process apoptotic process programmed cell death regulation of apoptotic signaling pathway response to hormone response to endogenous stimulus response to chemical response to estrogen cell adhesion cell-cell adhesion epithelial cell-cell adhesion regulation of integrin-mediated signaling pathway negative regulation of integrin-mediated signaling pathway integrin-mediated signaling pathway anatomical structure morphogenesis odontogenesis of dentin-containing tooth odontogenesis animal organ morphogenesis positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process positive regulation of extrinsic apoptotic signaling pathway in absence of ligand positive regulation of apoptotic signaling pathway positive regulation of response to stimulus positive regulation of cellular process positive regulation of programmed cell death positive regulation of extrinsic apoptotic signaling pathway positive regulation of apoptotic process positive regulation of signaling neuroblast proliferation negative regulation of neural precursor cell proliferation cellular developmental process regulation of developmental process regulation of neuroblast proliferation cell development regulation of cell differentiation regulation of neurogenesis regulation of cell development negative regulation of neuroblast proliferation regulation of nervous system development neurogenesis negative regulation of neurogenesis cell differentiation negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation regulation of neural precursor cell proliferation negative regulation of cell population proliferation regulation of multicellular organismal development cell population proliferation negative regulation of developmental process nervous system development generation of neurons negative regulation of cell development regulation of cell population proliferation neural precursor cell proliferation negative regulation of multicellular organismal process positive regulation of smoothened signaling pathway regulation of smoothened signaling pathway smoothened signaling pathway cellular component organization cellular component biogenesis cell junction organization cellular component assembly cell junction assembly cellular component organization or biogenesis apical junction assembly cell-cell junction assembly cell-cell junction organization cell migration cell motility negative regulation of locomotion regulation of cell motility regulation of locomotion negative regulation of cell motility locomotion female gonad development female sex differentiation development of primary female sexual characteristics ovarian follicle development gap junction assembly establishment or maintenance of cell polarity cell projection organization neuron projection development regeneration response to axon injury neuron projection regeneration axon regeneration neuron differentiation cellular response to stress response to stress response to wounding plasma membrane bounded cell projection organization axon development neuron development cellular response to nitrogen compound response to alcohol response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to indole-3-methanol cellular response to indole-3-methanol regulation of localization regulation of protein localization regulation of protein localization to nucleus protein localization to nucleus negative regulation of protein localization to nucleus localization macromolecule localization protein localization to organelle intracellular protein localization negative regulation of protein localization	cellular anatomical structure cell junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium cell-cell junction anchoring junction intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle cellular anatomical structure cell junction cell projection cell leading edge plasma membrane bounded cell projection lamellipodium cell-cell junction anchoring junction intracellular organelle intracellular anatomical structure cytoskeleton organelle membraneless organelle intracellular membraneless organelle actin cytoskeleton cell periphery plasma membrane membrane protein-containing complex extrinsic component of plasma membrane catenin complex plasma membrane protein complex membrane protein complex extrinsic component of membrane apical junction complex adherens junction zonula adherens membrane raft plasma membrane raft caveola membrane microdomain flotillin complex plasma membrane region membrane-bounded organelle Golgi apparatus cytoplasm intracellular membrane-bounded organelle endomembrane system intercalated disc cell-cell contact zone nucleus acrosomal vesicle intracellular vesicle cytoplasmic vesicle secretory granule secretory vesicle vesicle
A	Vinculin	small GTPase binding protein binding binding enzyme binding GTPase binding alpha-catenin binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding dystroglycan binding small GTPase binding protein binding binding enzyme binding GTPase binding alpha-catenin binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding dystroglycan binding structural molecule activity beta-catenin binding	regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion regulation of cellular process regulation of cellular component organization cell-substrate junction assembly cellular component organization cellular component biogenesis cell adhesion cellular component assembly cell junction assembly regulation of cell-substrate junction organization cellular component organization or biogenesis focal adhesion assembly regulation of biological process regulation of cell-substrate adhesion regulation of cell adhesion biological regulation cell-substrate adhesion regulation of cellular component biogenesis regulation of cell junction assembly cell junction organization cell-matrix adhesion regulation of cell-matrix adhesion cell-substrate junction organization cellular process regulation of focal adhesion assembly regulation of cell-substrate junction assembly cell-cell adhesion epithelial cell-cell adhesion lamellipodium assembly plasma membrane bounded cell projection organization cell projection organization plasma membrane bounded cell projection assembly lamellipodium organization cell projection assembly developmental process tissue morphogenesis anatomical structure morphogenesis epithelium development anatomical structure development morphogenesis of an epithelium tissue development apical junction assembly cell-cell junction assembly cell-cell junction organization regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion axon extension multicellular organismal process axonogenesis cellular developmental process developmental growth plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation system development neuron projection extension developmental cell growth growth nervous system development axon development cell morphogenesis involved in neuron differentiation developmental growth involved in morphogenesis generation of neurons neuron development adherens junction organization adherens junction assembly localization protein localization to cell surface macromolecule localization intracellular protein localization regulation of localization regulation of protein localization regulation of protein localization to cell-cell junction regulation of protein localization to adherens junction protein localization to adherens junction protein localization to cell-cell junction protein localization to cell junction regulation of establishment of endothelial barrier regulation of developmental process endothelium development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development regulation of endothelial cell development regulation of multicellular organismal process regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation epithelial cell development establishment of endothelial barrier	intracellular anatomical structure intracellular membraneless organelle Z disc sarcomere intracellular organelle I band cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer intracellular anatomical structure intracellular membraneless organelle Z disc sarcomere intracellular organelle I band cellular anatomical structure organelle membraneless organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex cell cortex cortical cytoskeleton actin cytoskeleton cell periphery cytoskeleton cortical actin cytoskeleton terminal web cell-cell junction anchoring junction cell junction podosome sarcolemma plasma membrane membrane costamere apical part of cell cluster of actin-based cell projections brush border adherens junction intercalated disc fascia adherens cell-cell contact zone desmosome inner dense plaque of desmosome actin filament bundle actomyosin stress fiber contractile actin filament bundle perinuclear region of cytoplasm polymeric cytoskeletal fiber actin filament podosome ring focal adhesion cell-substrate junction outer dense plaque of desmosome membrane microdomain membrane raft apical junction complex zonula adherens protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR001033	Alpha-catenin	Family
B	IPR036723	Alpha-catenin/vinculin-like superfamily	Homologous Superfamily
B	IPR006077	Vinculin/alpha-catenin	Family
B	IPR000633	Vinculin, conserved site	Conserved Site
A	IPR017997	Vinculin	Family
A	IPR036723	Alpha-catenin/vinculin-like superfamily	Homologous Superfamily
A	IPR006077	Vinculin/alpha-catenin	Family
A	IPR000633	Vinculin, conserved site	Conserved Site

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.