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- PDB-4ehp: Crystal Structure of human vinculin head domain (residues 1-252) ... -

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Basic information

Entry
Database: PDB / ID: 4ehp
TitleCrystal Structure of human vinculin head domain (residues 1-252) in complex with alpha-catenin (residues 277-382)
Components
  • Catenin alpha-1
  • Vinculin
KeywordsCELL ADHESION / adherens junctions / vinculin binding site / vinculin binding domain / helix bundle
Function / homology
Function and homology information


negative regulation of integrin-mediated signaling pathway / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / CDH11 homotypic and heterotypic interactions / podosome ring / Regulation of CDH19 Expression and Function / terminal web / Regulation of CDH11 function / cell-substrate junction ...negative regulation of integrin-mediated signaling pathway / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / CDH11 homotypic and heterotypic interactions / podosome ring / Regulation of CDH19 Expression and Function / terminal web / Regulation of CDH11 function / cell-substrate junction / gamma-catenin binding / epithelial cell-cell adhesion / zonula adherens / gap junction assembly / dystroglycan binding / cellular response to indole-3-methanol / alpha-catenin binding / fascia adherens / vinculin binding / cell-cell contact zone / flotillin complex / negative regulation of cell motility / apical junction assembly / costamere / adherens junction assembly / regulation of establishment of endothelial barrier / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of smoothened signaling pathway / catenin complex / Adherens junctions interactions / axon extension / protein localization to cell surface / negative regulation of protein localization to nucleus / lamellipodium assembly / axon regeneration / regulation of focal adhesion assembly / negative regulation of neuroblast proliferation / smoothened signaling pathway / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / Myogenesis / odontogenesis of dentin-containing tooth / brush border / intercalated disc / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / neuroblast proliferation / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / cell-matrix adhesion / acrosomal vesicle / VEGFR2 mediated vascular permeability / negative regulation of cell migration / cell projection / integrin-mediated signaling pathway / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / platelet aggregation / cell-cell adhesion / beta-catenin binding / response to estrogen / specific granule lumen / Signaling by RAF1 mutants / male gonad development / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin filament binding / Signaling by BRAF and RAF1 fusions / cell-cell junction / protein localization / Signaling by ALK fusions and activated point mutants / extracellular vesicle / cell migration / actin cytoskeleton / cell junction / Platelet degranulation / lamellipodium / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / intracellular membrane-bounded organelle / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Alpha-catenin / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) ...Alpha-catenin / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Vinculin / Catenin alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å
AuthorsIzard, T. / Rangarajan, E.S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: alpha-Catenin unfurls upon binding to vinculin
Authors: Rangarajan, E.S. / Izard, T.
History
DepositionApr 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vinculin
B: Catenin alpha-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,34911
Polymers40,8182
Non-polymers5319
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-41 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.250, 73.960, 107.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsTHE BIOLOGICAL UNIT COULD BE EITHER A HETERODIMER OR A TETRAMER IN SOLUTION.

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Components

#1: Protein Vinculin / Metavinculin


Mass: 28265.807 Da / Num. of mol.: 1 / Fragment: unp residues 1-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P18206
#2: Protein Catenin alpha-1 / Alpha E-catenin / Cadherin-associated protein / Renal carcinoma antigen NY-REN-13


Mass: 12552.145 Da / Num. of mol.: 1 / Fragment: unp residues 277-382
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNNA1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P35221
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: PEG 3350, sodium acetate, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.655→107.432 Å / Num. all: 13785 / Num. obs: 13785 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 58.8 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.068 / Net I/σ(I): 21.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.65-2.87.30.4851.61436519700.485100
2.8-2.977.30.3422.21375918800.342100
2.97-3.177.30.2133.61283217540.213100
3.17-3.437.30.1295.91192916340.129100
3.43-3.757.30.07410.41106115220.074100
3.75-4.27.20.04815.7992613800.048100
4.2-4.857.10.03519.7883912390.035100
4.85-5.9470.04216.1735710540.042100
5.94-8.46.80.0320.557558450.03100
8.4-107.4326.10.01825.530925070.01899.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.99 Å107.43 Å
Translation2.99 Å107.43 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
XSCALEdata scaling
BUSTER2.11.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IBF

2ibf


Resolution: 2.66→22.71 Å / Cor.coef. Fo:Fc: 0.9362 / Cor.coef. Fo:Fc free: 0.9156 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.545 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 686 5.03 %RANDOM
Rwork0.1925 ---
all0.247 13667 --
obs0.1944 13637 100 %-
Displacement parametersBiso max: 182.03 Å2 / Biso mean: 60.0904 Å2 / Biso min: 26.55 Å2
Baniso -1Baniso -2Baniso -3
1--12.478 Å20 Å20 Å2
2--6.1346 Å20 Å2
3---6.3435 Å2
Refine analyzeLuzzati coordinate error obs: 0.312 Å
Refinement stepCycle: LAST / Resolution: 2.66→22.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2672 0 36 82 2790
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011347SINUSOIDAL2
X-RAY DIFFRACTIONt_dihedral_angle_d1.0680HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion2.36390HARMONIC5
X-RAY DIFFRACTIONt_other_torsion3.322733HARMONIC20
X-RAY DIFFRACTIONt_trig_c_planes0.0067376SEMIHARMONIC5
X-RAY DIFFRACTIONt_gen_planes0.01261HARMONIC1
X-RAY DIFFRACTIONt_bcor1.4263326SEMIHARMONIC4
X-RAY DIFFRACTIONt_cont02733HARMONIC2
X-RAY DIFFRACTIONt_chiral03677HARMONIC2
LS refinement shellResolution: 2.66→2.87 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2792 174 6.32 %
Rwork0.2023 2580 -
all0.2071 2754 -
obs--100 %

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