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- PDB-1ydi: Human Vinculin Head Domain (VH1, 1-258) in Complex with Human Alp... -

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Basic information

Entry
Database: PDB / ID: 1ydi
TitleHuman Vinculin Head Domain (VH1, 1-258) in Complex with Human Alpha-Actinin's Vinculin-Binding Site (Residues 731-760)
Components
  • Alpha-actinin 4
  • vinculin isoform VCL
KeywordsCell Adhesion / Structural Protein
Function / homology
Function and homology information


positive regulation of sodium:proton antiporter activity / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / negative regulation of substrate adhesion-dependent cell spreading / terminal web / neutrophil degranulation / cell-substrate junction / platelet degranulation ...positive regulation of sodium:proton antiporter activity / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / negative regulation of substrate adhesion-dependent cell spreading / terminal web / neutrophil degranulation / cell-substrate junction / platelet degranulation / epithelial cell-cell adhesion / zonula adherens / nucleoside binding / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / muscle cell development / adherens junction assembly / apical junction assembly / vesicle transport along actin filament / costamere / nuclear retinoic acid receptor binding / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / podosome / Nephrin family interactions / lamellipodium assembly / regulation of focal adhesion assembly / cortical actin cytoskeleton / maintenance of blood-brain barrier / pseudopodium / brush border / Smooth Muscle Contraction / retinoic acid receptor signaling pathway / stress fiber / tumor necrosis factor-mediated signaling pathway / peroxisome proliferator activated receptor signaling pathway / negative regulation of cell migration / cell-matrix adhesion / nuclear receptor coactivator activity / platelet alpha granule lumen / cell projection / muscle contraction / morphogenesis of an epithelium / nuclear receptor binding / adherens junction / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / chromatin DNA binding / sarcolemma / beta-catenin binding / platelet aggregation / Z disc / positive regulation of non-canonical NF-kappaB signal transduction / specific granule lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / extracellular vesicle / actin filament binding / Signaling by ALK fusions and activated point mutants / protein transport / actin cytoskeleton / integrin binding / Platelet degranulation / cell junction / actin binding / actin cytoskeleton organization / regulation of apoptotic process / secretory granule lumen / ficolin-1-rich granule lumen / transmembrane transporter binding / molecular adaptor activity / transcription coactivator activity / cytoskeleton / cell adhesion / positive regulation of cell migration / ribonucleoprotein complex / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / calcium ion binding / Neutrophil degranulation / structural molecule activity / perinuclear region of cytoplasm / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand ...Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Alpha-catenin/vinculin-like superfamily / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-actinin-4 / Vinculin / Vinculin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsIzard, T.
CitationJournal: Mol.Cell.Biol. / Year: 2005
Title: Structural Dynamics of {alpha}-Actinin-Vinculin Interactions.
Authors: Bois, P.R. / Borgon, R.A. / Vonrhein, C. / Izard, T.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: vinculin isoform VCL
B: Alpha-actinin 4


Theoretical massNumber of molelcules
Total (without water)32,4282
Polymers32,4282
Non-polymers00
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-26 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.843, 54.268, 63.598
Angle α, β, γ (deg.)90.00, 107.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein vinculin isoform VCL


Mass: 29628.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEt3 / Production host: Escherichia coli (E. coli) / References: UniProt: P18206-2, UniProt: P18206*PLUS
#2: Protein/peptide Alpha-actinin 4 / Non-muscle alpha-actinin 4 / F-actin cross linking protein


Mass: 2800.170 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTN4 / Production host: Escherichia coli (E. coli) / References: UniProt: O43707
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.41 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→40.5 Å / Num. obs: 24098 / Biso Wilson estimate: 20.2 Å2

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Processing

SoftwareName: BUSTER-TNT / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.42 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1192 5 %RANDOM
Rwork0.171 ---
obs0.181 24098 92.9 %-
all-24098 --
Displacement parametersBiso mean: 17.13 Å2
Baniso -1Baniso -2Baniso -3
1--3.48 Å20 Å20.22 Å2
2---1.23 Å20 Å2
3---4.72 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 0 466 2725
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00522912
X-RAY DIFFRACTIONt_angle_deg0.8930942
X-RAY DIFFRACTIONt_dihedral_angle_d14.62214030
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005702
X-RAY DIFFRACTIONt_gen_planes0.013145
X-RAY DIFFRACTIONt_it1.342229320
X-RAY DIFFRACTIONt_nbd
LS refinement shellResolution: 1.57→1.66 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2735 31 5.1 %
Rwork0.218 576 -
obs--10.3 %

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