1YDI

Human Vinculin Head Domain (VH1, 1-258) in Complex with Human Alpha-Actinin's Vinculin-Binding Site (Residues 731-760)

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1ydia1	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	d1ydia3	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A	SCOP2B Superfamily	alpha-Catenin/Vinculin-like	8039803	3001619	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	alpha-Catenin/Vinculin-like	8039802	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)
A	Vinculin_1st	e1ydiA5	A: alpha bundles	X: Four-helical up-and-down bundle	H: alpha-catenin-related	T: alpha-catenin/vinculin	F: Vinculin_1st	ECOD (1.6)

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
B	PF00435	Spectrin repeat (Spectrin)	Spectrin repeat	Spectrin repeat-domains are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference [2]. The spectr ...	Spectrin repeat-domains are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference [2]. The spectrin domain- repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C. Although the domain occurs in multiple repeats along sequences, the domains are actually stable on their own - ie they act, biophysically, like domains rather than repeats that along function when aggregated.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	vinculin isoform VCL	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 protein localization localization cellular localization protein localization to cell surface cellular macromolecule localization macromolecule 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 regulation of cellular localization 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 cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton terminal web cytoplasm non-membrane-bounded organelle intracellular anatomical structure cell cortex cortical cytoskeleton cellular anatomical entity actin cytoskeleton intracellular organelle cell periphery cytoskeleton organelle intracellular non-membrane-bounded organelle cortical actin cytoskeleton terminal web cytoplasm non-membrane-bounded organelle 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 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 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 cell projection
B	Alpha-actinin 4	cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding transcription coactivator activity transcription regulator activity transcription coregulator activity cytoskeletal protein binding actin binding protein-containing complex binding protein binding binding actin filament binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding transcription coactivator activity transcription regulator activity transcription coregulator activity nuclear receptor coactivator activity protein-macromolecule adaptor activity molecular adaptor activity cation binding ion binding calcium ion binding metal ion binding transcription factor binding nuclear retinoic acid receptor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding RNA binding nucleic acid binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding transmembrane transporter binding cell adhesion molecule binding integrin binding signaling receptor binding identical protein binding protein homodimerization activity protein dimerization activity chromatin binding chromatin DNA binding	regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation cellular process apoptotic process regulation of programmed cell death cell death programmed cell death cellular response to stimulus intracellular receptor signaling pathway response to stimulus signaling retinoic acid receptor signaling pathway regulation of biological process regulation of cellular process regulation of apoptotic process biological regulation cellular process apoptotic process regulation of programmed cell death cell death programmed cell death cellular response to stimulus intracellular receptor signaling pathway response to stimulus signaling retinoic acid receptor signaling pathway cell communication signal transduction cellular component organization organelle organization actin cytoskeleton organization actin filament-based process cellular component organization or biogenesis cytoskeleton organization regulation of localization positive regulation of cation transmembrane transport sodium ion transmembrane transport regulation of sodium ion transport regulation of sodium ion transmembrane transport positive regulation of sodium ion transport localization positive regulation of monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation transport regulation of monoatomic ion transport proton transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport regulation of molecular function regulation of transmembrane transport transport positive regulation of sodium ion transmembrane transporter activity monoatomic ion transmembrane transport positive regulation of biological process regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport metal ion transport regulation of transporter activity monoatomic cation transmembrane transport regulation of sodium ion transmembrane transporter activity positive regulation of molecular function positive regulation of transmembrane transport positive regulation of sodium ion transmembrane transport monoatomic ion transport regulation of metal ion transport positive regulation of cellular process regulation of monoatomic ion transmembrane transporter activity regulation of proton transport regulation of transport positive regulation of sodium:proton antiporter activity regulation of sodium:proton antiporter activity positive regulation of transport positive regulation of transporter activity positive regulation of ion transmembrane transporter activity regulation of monoatomic cation transmembrane transport sodium ion transport peroxisome proliferator activated receptor signaling pathway response to organic substance cell surface receptor signaling pathway response to cytokine cytokine-mediated signaling pathway cellular response to chemical stimulus cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus cellular response to organic substance response to tumor necrosis factor developmental process muscle structure development muscle cell development cellular developmental process cell differentiation anatomical structure development cell development muscle cell differentiation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process protein localization establishment of protein localization cellular localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization regulation of cell-substrate adhesion regulation of cell adhesion regulation of substrate adhesion-dependent cell spreading negative regulation of biological process cell-substrate adhesion negative regulation of cell adhesion cell adhesion negative regulation of substrate adhesion-dependent cell spreading negative regulation of cellular process substrate adhesion-dependent cell spreading negative regulation of cell-substrate adhesion positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette regulation of signaling non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling vesicle transport along actin filament vesicle cytoskeletal trafficking vesicle localization establishment of organelle localization establishment of vesicle localization intracellular transport actin filament-based movement organelle localization establishment of localization in cell cytoskeleton-dependent intracellular transport actin filament-based transport	cell projection pseudopodium cellular anatomical entity plasma membrane bounded cell projection intracellular anatomical structure Z disc sarcomere intracellular organelle I band organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber cell projection pseudopodium cellular anatomical entity plasma membrane bounded cell projection intracellular anatomical structure Z disc sarcomere intracellular organelle I band organelle intracellular non-membrane-bounded organelle contractile muscle fiber cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytoskeleton actin cytoskeleton actin filament bundle actomyosin stress fiber contractile actin filament bundle 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 secretory granule secretory vesicle platelet alpha granule platelet alpha granule lumen cell junction anchoring junction focal adhesion cell-substrate junction cell periphery plasma membrane membrane protein-containing complex cell cortex cortical cytoskeleton cortical actin cytoskeleton ribonucleoprotein complex nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
B	IPR002048	EF-hand domain	Domain
B	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
B	IPR001589	Actinin-type actin-binding domain, conserved site	Conserved Site
B	IPR036872	CH domain superfamily	Homologous Superfamily
B	IPR002017	Spectrin repeat	Repeat
B	IPR001715	Calponin homology domain	Domain
B	IPR014837	EF-hand, Ca insensitive	Domain
B	IPR011992	EF-hand domain pair	Homologous Superfamily
B	IPR018159	Spectrin/alpha-actinin	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	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
B	Pharos: O43707	sarcomatoid carcinoma focal segmental glomerulosclerosis 1 carcinoma Mammary Neoplasms, Experimental focal segmental glomerulosclerosis acute myeloid leukemia astrocytic tumor drug-induced liver injury mammary neoplasms, animal pancreatic ductal adenocarcinoma psoriasis pancreatic intraductal papillary-mucinous neoplasm rheumatoid arthritis undifferentiated carcinoma ovarian cancer sarcomatoid carcinoma focal segmental glomerulosclerosis 1 carcinoma Mammary Neoplasms, Experimental focal segmental glomerulosclerosis acute myeloid leukemia astrocytic tumor drug-induced liver injury mammary neoplasms, animal pancreatic ductal adenocarcinoma psoriasis pancreatic intraductal papillary-mucinous neoplasm rheumatoid arthritis undifferentiated carcinoma ovarian cancer proteinuria

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.