3RF3 | pdb_00003rf3

Shigella IpaA-VBS3 in complex with human vinculin

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3rf3b1	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin-like	alpha-catenin/vinculin	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rf3a1	All alpha proteins	Four-helical up-and-down bundle	alpha-catenin/vinculin-like	alpha-catenin/vinculin	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	alpha-Catenin/Vinculin-like	8039803	3001619	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha-Catenin/Vinculin-like	8039802	3001619	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	alpha-Catenin/Vinculin-like	8039802	3001619	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	alpha-Catenin/Vinculin-like	8039803	3001619	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)
B	Vinculin	e3rf3B5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Vinculin	ECOD (develop294)
A	Vinculin	e3rf3A5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Vinculin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.120.230	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Alpha-catenin/vinculin-like	CATH (4.3.0)
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
C, D	PF17985	SipA vinculin binding site (SipA_VBS)	SipA vinculin binding site	-	Motif
A, B	PF01044	Vinculin family (Vinculin)	Vinculin family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	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, B	Vinculin	protein binding binding alpha-catenin binding cell adhesion molecule binding cadherin binding molecular adaptor activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding dystroglycan binding cytoskeletal protein binding actin 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 multicellular organismal process regulation of body fluid levels wound healing response to stimulus homotypic cell-cell adhesion cell activation hemostasis platelet aggregation blood coagulation response to stress coagulation regulation of biological quality response to wounding platelet activation apical junction assembly cell-cell junction assembly cell-cell junction organization 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 axon extension 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 maintenance of blood-brain barrier multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis	intracellular anatomical structure cell cortex cortical cytoskeleton intracellular membraneless organelle actin cytoskeleton intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle cortical actin cytoskeleton terminal web cytoplasm intracellular anatomical structure cell cortex cortical cytoskeleton intracellular membraneless organelle actin cytoskeleton intracellular organelle cell periphery cellular anatomical structure cytoskeleton organelle membraneless organelle cortical actin cytoskeleton terminal web cytoplasm cell-cell junction anchoring junction cell junction extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol sarcolemma plasma membrane membrane costamere contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex apical part of cell cluster of actin-based cell projections brush border adherens junction intercalated disc fascia adherens cell-cell contact zone cell-substrate junction desmosome inner dense plaque of desmosome perinuclear region of cytoplasm vesicle lumen intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen cytoplasmic vesicle organelle lumen specific granule lumen secretory granule secretory vesicle specific granule podosome podosome ring focal adhesion outer dense plaque of desmosome membrane microdomain membrane raft apical junction complex zonula adherens ficolin-1-rich granule ficolin-1-rich granule lumen protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR015138	Salmonella invasion protein A, N-terminal	Domain
C, D	IPR023225	Salmonella invasion protein A, chaperone-binding	Homologous Superfamily
C, D	IPR040658	SipA, vinculin binding site	Conserved Site
A, B	IPR017997	Vinculin	Family
A, B	IPR036723	Alpha-catenin/vinculin-like superfamily	Homologous Superfamily
A, B	IPR006077	Vinculin/alpha-catenin	Family
A, B	IPR000633	Vinculin, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P18206	dilated cardiomyopathy 1W hypertrophic cardiomyopathy 15 dilated cardiomyopathy osteoporosis acute coronary syndrome cardiomyopathy hypertrophic cardiomyopathy malignant ependymoma ovarian cancer spondyloarthropathy Crohn disease familial isolated dilated cardiomyopathy lung carcinoma malignant pancreatic neoplasm Osteoporosis, Age-Related dilated cardiomyopathy 1W hypertrophic cardiomyopathy 15 dilated cardiomyopathy osteoporosis acute coronary syndrome cardiomyopathy hypertrophic cardiomyopathy malignant ependymoma ovarian cancer spondyloarthropathy Crohn disease familial isolated dilated cardiomyopathy lung carcinoma malignant pancreatic neoplasm Osteoporosis, Age-Related pancreatic ductal adenocarcinoma subependymal giant cell astrocytoma astrocytic tumor Charcot-Marie-Tooth disease diabetes mellitus familial dilated cardiomyopathy glioblastoma inflammatory bowel disease malignant colon neoplasm medulloblastoma tuberculosis atypical teratoid rhabdoid tumor familial hypertrophic cardiomyopathy lung cancer

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.