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

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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 / homologySignaling by high-kinase activity BRAF mutants / Platelet degranulation / Vinculin, conserved site / Alpha-catenin / Vinculin/alpha-catenin / Vinculin / Alpha E-catenin / Alpha-catenin/vinculin-like superfamily / Vinculin family / Vinculin family talin-binding region signature. ...Signaling by high-kinase activity BRAF mutants / Platelet degranulation / Vinculin, conserved site / Alpha-catenin / Vinculin/alpha-catenin / Vinculin / Alpha E-catenin / Alpha-catenin/vinculin-like superfamily / Vinculin family / Vinculin family talin-binding region signature. / Signaling by RAS mutants / Signaling by BRAF and RAF fusions / Vinculin repeated domain signature. / Paradoxical activation of RAF signaling by kinase inactive BRAF / VEGFR2 mediated vascular permeability / Signaling by moderate kinase activity BRAF mutants / Neutrophil degranulation / MAP2K and MAPK activation / CDO in myogenesis / RHO GTPases activate IQGAPs / Smooth Muscle Contraction / Adherens junctions interactions / negative regulation of integrin-mediated signaling pathway / gap junction assembly / cell-substrate junction / negative regulation of neuroblast proliferation / inner dense plaque of desmosome / outer dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / gamma-catenin binding / adherens junction assembly / flotillin complex / cellular response to indole-3-methanol / fascia adherens / apical junction assembly / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / vinculin binding / positive regulation of smoothened signaling pathway / alpha-catenin binding / negative regulation of cell motility / catenin complex / establishment or maintenance of cell polarity / costamere / protein localization to cell surface / lamellipodium assembly / axon regeneration / podosome / intercalated disc / adherens junction organization / brush border / extracellular vesicle / adherens junction / cellular protein localization / positive regulation of muscle cell differentiation / axon extension / negative regulation of cell migration / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ovarian follicle development / actin filament organization / cell-cell adherens junction / muscle contraction / acrosomal vesicle / cell-matrix adhesion / platelet aggregation / sarcolemma / morphogenesis of an epithelium / odontogenesis of dentin-containing tooth / actin cytoskeleton / protein heterooligomerization / beta-catenin binding / cell-cell junction / male gonad development / platelet degranulation / lamellipodium / actin filament binding / specific granule lumen / actin binding / cell / secretory granule lumen / cytoskeleton / ficolin-1-rich granule lumen / response to estrogen / cadherin binding / aging / cell junction / cell adhesion / membrane raft / intracellular membrane-bounded organelle / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / neutrophil degranulation / protein heterodimerization activity / Golgi apparatus / protein-containing complex / RNA binding / extracellular exosome
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / 2.66 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 3, 2012 / Release: Apr 18, 2012
RevisionDateData content typeGroupProviderType
1.0Apr 18, 2012Structure modelrepositoryInitial release
1.1Jul 17, 2013Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,34911
Polyers40,8182
Non-polymers5319
Water1,47782
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)6250
ΔGint (kcal/M)-41
Surface area (Å2)19600
MethodPISA
Unit cell
γ
α
β
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-MP 21 21 2
DetailsTHE BIOLOGICAL UNIT COULD BE EITHER A HETERODIMER OR A TETRAMER IN SOLUTION.

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Components

#1: Protein/peptide Vinculin / / Metavinculin


Mass: 28265.807 Da / Num. of mol.: 1 / Fragment: unp residues 1-252 / Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid name: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P18206
#2: Protein/peptide 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: (gene. exp.) Homo sapiens (human) / Gene: CTNNA1 / Plasmid name: 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 / Formula: C2H3O2 / Acetate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Formula: H2O / Water

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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 / Density percent sol: 55.85 %
Crystal growTemp: 295 K / Method: vapor diffusion
Details: PEG 3350, sodium acetate, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: APS BEAMLINE 22-BM / Synchrotron site: APS / Beamline: 22-BM / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Collection date: Oct 21, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 58.8 Å2 / D resolution high: 2.655 Å / D resolution low: 107.432 Å / Number all: 13785 / Number obs: 13785 / Observed criterion sigma F: 1 / Observed criterion sigma I: 1 / Rmerge I obs: 0.089 / Rsym value: 0.068 / NetI over sigmaI: 21.2 / Redundancy: 7.2 % / Percent possible obs: 100
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionMeanI over sigI obsNumber measured allNumber unique allRsym valueRedundancyPercent possible all
0.4852.6502.8001.6001436519700.4857.300100.000
0.3422.8002.9702.2001375918800.3427.300100.000
0.2132.9703.1703.6001283217540.2137.300100.000
0.1293.1703.4305.9001192916340.1297.300100.000
0.0743.4303.75010.4001106115220.0747.300100.000
0.0483.7504.20015.700992613800.0487.200100.000
0.0354.2004.85019.700883912390.0357.100100.000
0.0424.8505.94016.100735710540.0427.000100.000
0.0305.9408.40020.50057558450.0306.800100.000
0.0188.400107.43225.50030925070.0186.10099.900

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Phasing

PhasingMethod: molecular replacement
Phasing MRD res high rotation: 2.99 / D res high translation: 2.99 / D res low rotation: 107.43 / D res low translation: 107.43

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Processing

Software
NameVersionClassificationContact authorContact author emailDateLanguageLocationType
SCALA3.3.16data scalingPhil R. Evanspre[at]mrc-lmb.cam.ac.uk2010/01/06Fortran_77http://www.ccp4.ac.uk/dist/html/scala.htmlother
MOLREPphasingAlexei Vaguinealexei[at]ysbl.york.ac.ukFortran_77http://www.ccp4.ac.uk/dist/html/molrep.htmlprogram
BUSTER-TNTrefinementGerard Bricognebuster-develop[at]GlobalPhasing.comhttp://www.globalphasing.com/buster/program
PDB_EXTRACT3.10data extractionPDBdeposit[at]deposit.rcsb.orgJune 10, 2010C++http://sw-tools.pdb.org/apps/PDB_EXTRACT/package
SERGUIdata collection
XSCALEdata scaling
BUSTER2.11.2refinement
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IBF
Correlation coeff Fo to Fc: 0.9362 / Correlation coeff Fo to Fc free: 0.9156 / Occupancy max: 1 / Occupancy min: 0 / Overall SU R Cruickshank DPI: 0.545 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Stereochemistry target values: Engh & Huber
Displacement parametersB iso max: 182.03 Å2 / B iso mean: 60.0904 Å2 / B iso min: 26.55 Å2 / Aniso B11: -12.478 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: 6.1346 Å2 / Aniso B23: 0 Å2 / Aniso B33: 6.3435 Å2
Least-squares processR factor R free: 0.2294 / R factor R work: 0.1925 / R factor all: 0.247 / R factor obs: 0.1944 / Highest resolution: 2.66 Å / Lowest resolution: 22.71 Å / Number reflection R free: 686 / Number reflection all: 13667 / Number reflection obs: 13637 / Percent reflection R free: 5.03 / Percent reflection obs: 1
Refine analyzeLuzzati coordinate error obs: 0.312 Å
Refine hist #LASTHighest resolution: 2.66 Å / Lowest resolution: 22.71 Å
Number of atoms included #LASTProtein: 2672 / Nucleic acid: 0 / Ligand: 36 / Solvent: 82 / Total: 2790
Refine LS restraints
Refine IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0101347SINUSOIDAL2.000
X-RAY DIFFRACTIONt_dihedral_angle_d1.06080HARMONIC2.000
X-RAY DIFFRACTIONt_omega_torsion2.360390HARMONIC5.000
X-RAY DIFFRACTIONt_other_torsion3.322733HARMONIC20.000
X-RAY DIFFRACTIONt_trig_c_planes0.0067376SEMIHARMONIC5.000
X-RAY DIFFRACTIONt_gen_planes0.01261HARMONIC1.000
X-RAY DIFFRACTIONt_bcor1.4263326SEMIHARMONIC4.000
X-RAY DIFFRACTIONt_cont02733HARMONIC2.000
X-RAY DIFFRACTIONt_chiral03677HARMONIC2.000
Refine LS shellHighest resolution: 2.66 Å / R factor R free: 0.2792 / R factor R work: 0.2023 / R factor all: 0.2071 / Lowest resolution: 2.87 Å / Number reflection R free: 174 / Number reflection R work: 2580 / Number reflection all: 2754 / Total number of bins used: 7 / Percent reflection R free: 6.32 / Percent reflection obs: 100

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