2GDC | pdb_00002gdc

Structure of Vinculin VD1 / IpaA560-633 complex

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	d2gdca1	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin-like	alpha-catenin/vinculin	automated matches	chicken (Gallus gallus ) [TaxId: 9031 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PCNA_N	e2gdcA2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: PCNA_N	ECOD (v294.1)
A	ALO	e2gdcA4	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ALO	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
B	PF17985	SipA vinculin binding site (SipA_VBS)	SipA vinculin binding site	-	Motif
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	Invasin ipaA	cytoskeletal protein binding protein binding binding vinculin binding actin binding	positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size positive regulation of biological process protein-containing complex disassembly positive regulation of actin filament depolymerization regulation of protein-containing complex disassembly actin filament depolymerization cellular component organization regulation of actin filament depolymerization actin filament-based process positive regulation of organelle organization regulation of cytoskeleton organization regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization regulation of actin filament-based process regulation of cellular component size positive regulation of biological process protein-containing complex disassembly positive regulation of actin filament depolymerization regulation of protein-containing complex disassembly actin filament depolymerization cellular component organization regulation of actin filament depolymerization actin filament-based process cellular component organization or biogenesis regulation of biological quality positive regulation of protein-containing complex disassembly positive regulation of cellular process cellular component disassembly actin polymerization or depolymerization regulation of biological process regulation of actin filament organization actin cytoskeleton organization protein-containing complex organization regulation of protein depolymerization positive regulation of protein depolymerization positive regulation of cytoskeleton organization biological regulation actin filament organization regulation of actin polymerization or depolymerization positive regulation of supramolecular fiber organization regulation of organelle organization organelle organization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization cellular process supramolecular fiber organization protein depolymerization cytoskeleton organization regulation of anatomical structure size	cellular anatomical structure extracellular region
A	Vinculin	protein binding binding alpha-catenin binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding alpha-actinin binding actinin binding muscle alpha-actinin binding cell adhesion molecule binding cadherin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding protein binding binding alpha-catenin binding cytoskeletal protein binding actin binding protein-containing complex binding actin filament binding alpha-actinin binding actinin binding muscle alpha-actinin binding cell adhesion molecule binding cadherin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding vinculin binding dystroglycan binding scaffold protein binding identical protein binding protein homodimerization activity protein dimerization activity 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 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 neuromuscular junction synapse desmosome inner dense plaque of desmosome actin filament bundle actomyosin stress fiber contractile actin filament bundle perinuclear region of cytoplasm podosome podosome ring muscle tendon junction cell-substrate junction membrane-bounded organelle mitochondrial membrane organelle inner membrane mitochondrion intracellular membrane-bounded organelle mitochondrial inner membrane organelle envelope mitochondrial envelope organelle membrane skeletal muscle myofibril focal adhesion outer dense plaque of desmosome apical junction complex zonula adherens protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR015138	Salmonella invasion protein A, N-terminal	Domain
B	IPR023225	Salmonella invasion protein A, chaperone-binding	Homologous Superfamily
B	IPR040658	SipA, vinculin binding 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.