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- PDB-5l0i: Human metavinculin MVt R975W cardiomyopathy-associated mutant (re... -

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Basic information

Entry
Database: PDB / ID: 5l0i
TitleHuman metavinculin MVt R975W cardiomyopathy-associated mutant (residues 959-1134)
ComponentsVinculin
KeywordsCELL ADHESION / 5-Helix bundle / cytoskeletal protein / cardiomyopathy
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 / adherens junction assembly / protein localization to cell surface / 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-matrix adhesion / morphogenesis of an epithelium / cell projection / 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 / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / secretory granule lumen / molecular adaptor activity / ficolin-1-rich granule lumen / 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: 2.45 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7643
Polymers19,6491
Non-polymers1152
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint-6 kcal/mol
Surface area9160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.074, 41.519, 44.148
Angle α, β, γ (deg.)90.00, 96.14, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Vinculin / Metavinculin / MV


Mass: 19648.713 Da / Num. of mol.: 1 / Fragment: UNP Residues 959-1134 / Mutation: R975W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18206
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.1 Å3/Da / Density % sol: 41.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na-citrate tribasic dihydrate, 2% Tacsimate (pH 5), and 16% PEG 3350

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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: Oct 7, 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: 2.45→44.78 Å / Num. obs: 5966 / % possible obs: 98 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.66 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.023 / Net I/σ(I): 49.2
Reflection shellResolution: 2.45→2.55 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 37 / CC1/2: 0.998 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MYI

3myi


Resolution: 2.45→44.78 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.8815 / SU R Cruickshank DPI: 1.208 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 2.924 / SU Rfree Blow DPI: 0.287 / SU Rfree Cruickshank DPI: 0.287
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 295 4.94 %RANDOM
Rwork0.1948 ---
obs0.1969 5966 97.69 %-
Displacement parametersBiso mean: 39.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.3412 Å20 Å27.2742 Å2
2---7.5744 Å20 Å2
3---7.2333 Å2
Refine analyzeLuzzati coordinate error obs: 0.281 Å
Refinement stepCycle: 1 / Resolution: 2.45→44.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1363 0 7 66 1436
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011383HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.11863HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d518SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes195HARMONIC5
X-RAY DIFFRACTIONt_it1383HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion18.09
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion196SEMIHARMONIC5
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_contact1684SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.74 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2546 85 4.99 %
Rwork0.2009 1618 -
all0.2037 1703 -
obs--97.69 %

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