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- PDB-5l0j: Human vinculin R903Q, D907R, R910T mutant(residues 891-1066) -

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Basic information

Entry
Database: PDB / ID: 5l0j
TitleHuman vinculin R903Q, D907R, R910T mutant(residues 891-1066)
ComponentsVinculin
KeywordsCELL ADHESION / 5-Helix bundle / cytoskelatal protein / phospholipids / structural protein
Function / homology
Function and homology information


regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / fascia adherens / dystroglycan binding ...regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / fascia adherens / dystroglycan binding / alpha-catenin binding / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / adherens junction assembly / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / negative regulation of cell migration / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell projection / morphogenesis of an epithelium / cell-matrix adhesion / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / platelet aggregation / 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 / cell-cell junction / Signaling by BRAF and RAF1 fusions / Signaling by ALK fusions and activated point mutants / Platelet degranulation / extracellular vesicle / actin binding / secretory granule lumen / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / ficolin-1-rich granule lumen / molecular adaptor activity / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol
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 / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsChinthalapudi, K. / Izard, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Differential lipid binding of vinculin isoforms promotes quasi-equivalent dimerization.
Authors: Chinthalapudi, K. / Rangarajan, E.S. / Brown, D.T. / Izard, T.
History
DepositionJul 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vinculin
B: Vinculin


Theoretical massNumber of molelcules
Total (without water)39,4342
Polymers39,4342
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-5 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.430, 86.430, 175.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Vinculin / Metavinculin / MV


Mass: 19716.922 Da / Num. of mol.: 2 / Mutation: R903Q, D907R, R910T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18206
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 4.79 Å3/Da / Density % sol: 74.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium (pH 7.5), and 1.5 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 4→175.2 Å / Num. obs: 6727 / % possible obs: 98.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 105.45 Å2 / Rpim(I) all: 0.043 / Net I/σ(I): 13.3
Reflection shellResolution: 4→4.22 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.9 / CC1/2: 0.896 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RKE

1rke


Resolution: 4→23.79 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.853 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.747
RfactorNum. reflection% reflectionSelection details
Rfree0.298 318 4.78 %RANDOM
Rwork0.293 ---
obs0.293 6653 98.1 %-
Displacement parametersBiso mean: 158.99 Å2
Baniso -1Baniso -2Baniso -3
1--31.8169 Å20 Å20 Å2
2---31.8169 Å20 Å2
3---63.6337 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: LAST / Resolution: 4→23.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2564 0 0 16 2580
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012581HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.183460HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d990SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes362HARMONIC5
X-RAY DIFFRACTIONt_it2581HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.2
X-RAY DIFFRACTIONt_other_torsion22.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion369SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3237SEMIHARMONIC4
LS refinement shellResolution: 4→4.47 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.322 -4.21 %
Rwork0.317 1776 -
all0.317 1854 -
obs--98.3 %

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