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- PDB-1rke: Human vinculin head (1-258) in complex with human vinculin tail (... -

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Basic information

Entry
Database: PDB / ID: 1rke
TitleHuman vinculin head (1-258) in complex with human vinculin tail (879-1066)
Components
  • VCL protein
  • Vinculin
Keywordscell adhesion / structural protein / cytoskeleton / actin-binding / x-ray crystallography
Function / homologyVinculin family talin-binding region signature. / Vinculin family / Alpha-catenin/vinculin-like superfamily / Vinculin / Vinculin/alpha-catenin / Platelet degranulation / Vinculin, conserved site / Smooth Muscle Contraction / MAP2K and MAPK activation / Neutrophil degranulation ...Vinculin family talin-binding region signature. / Vinculin family / Alpha-catenin/vinculin-like superfamily / Vinculin / Vinculin/alpha-catenin / Platelet degranulation / Vinculin, conserved site / Smooth Muscle Contraction / MAP2K and MAPK activation / Neutrophil degranulation / Signaling by moderate kinase activity BRAF mutants / Signaling by high-kinase activity BRAF mutants / Signaling by RAS mutants / Signaling by BRAF and RAF fusions / Paradoxical activation of RAF signaling by kinase inactive BRAF / Vinculin repeated domain signature. / cell-substrate junction / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / adherens junction assembly / fascia adherens / apical junction assembly / alpha-catenin binding / costamere / protein localization to cell surface / lamellipodium assembly / podosome / brush border / extracellular vesicle / adherens junction / axon extension / negative regulation of cell migration / cell-cell adherens junction / muscle contraction / cell-matrix adhesion / platelet aggregation / sarcolemma / morphogenesis of an epithelium / beta-catenin binding / cell-cell junction / platelet degranulation / actin binding / specific granule lumen / cell / secretory granule lumen / cytoskeleton / ficolin-1-rich granule lumen / cadherin binding / cell adhesion / membrane raft / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / neutrophil degranulation / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytosol / Vinculin
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / 2.35 Å resolution
AuthorsIzard, T. / Evans, G. / Borgon, R.A. / Rush, C.L. / Bricogne, G. / Bois, P.R.
CitationJournal: Nature / Year: 2004
Title: Vinculin activation by talin through helical bundle conversion
Authors: Izard, T. / Evans, G. / Borgon, R.A. / Rush, C.L. / Bricogne, G. / Bois, P.R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 21, 2003 / Release: Jan 13, 2004
RevisionDateData content typeGroupProviderType
1.0Jan 13, 2004Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vinculin
B: VCL protein


Theoretical massNumber of molelcules
Total (without water)50,3252
Polyers50,3252
Non-polymers00
Water3,675204
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)2620
ΔGint (kcal/M)-13
Surface area (Å2)21240
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)86.603, 161.648, 36.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP 21 21 2

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Components

#1: Protein/peptide Vinculin /


Mass: 29489.982 Da / Num. of mol.: 1 / Fragment: vinculin head (residues 1-258) / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Gene: VCL / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P18206
#2: Protein/peptide VCL protein


Mass: 20835.076 Da / Num. of mol.: 1 / Fragment: vinculin tail (residues 879-1066) / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P18206
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 / Density percent sol: 46 %
Crystal growTemp: 293 K / pH: 8
Details: 15% PEG 3350; 50 mM NaCl; 100 mM Tris (pH 8); 10 mM DTT, pH 8.0, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
components of the solutions
*PLUS

Crystal ID: 1 / Sol ID: reservoir

IDConcCommon nameChemical formulaDetails
115 %PEG3350
250 mMNaCl
3100 mMTrispH8
410 mMdithiothreitol

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Data collection

SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 5.0.2 / Synchrotron site: ALS / Beamline: 5.0.2 / Wavelength: 0.9797
DetectorDetector: CCD
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 37.5 Å2 / D resolution high: 2.35 Å / D resolution low: 99.8 Å / Number all: 21798 / Number obs: 21798 / Observed criterion sigma I: 0

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Processing

Software
NameVersionClassification
d*TREKdata scaling
SCALAdata scaling
SHARPphasing
BUSTER-TNTrefinement
d*TREKdata reduction
CCP4(SCALA)data scaling
RefineMethod to determine structure: SIRAS / R Free selection details: RANDOM / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0 / Sigma I: 0
Displacement parametersB iso mean: 56.2 Å2 / Aniso B11: 13 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -5.4 Å2 / Aniso B23: 0 Å2 / Aniso B33: -7.6 Å2
Least-squares processR factor R free: 0.278 / R factor R work: 0.206 / Highest resolution: 2.35 Å / Lowest resolution: 15 Å / Number reflection R free: 1118 / Number reflection all: 21798 / Number reflection obs: 21798 / Percent reflection R free: 5.1 / Percent reflection obs: 99.8
Refine hist #LASTHighest resolution: 2.35 Å / Lowest resolution: 15 Å
Number of atoms included #LASTProtein: 3456 / Nucleic acid: 0 / Ligand: 0 / Solvent: 204 / Total: 3660
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_angle_deg0.979
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refine LS shellHighest resolution: 2.35 Å / R factor R free: 0.277 / R factor R work: 0.205 / Lowest resolution: 2.42 Å / Total number of bins used: 9
Least-squares process
*PLUS
Lowest resolution: 15 Å / Number reflection all: 20680 / Percent reflection R free: 5

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