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- PDB-5l0f: Human metavinculin quadruple mutant (residues 959-1134) -

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Basic information

Entry
Database: PDB / ID: 5l0f
TitleHuman metavinculin quadruple mutant (residues 959-1134)
ComponentsVinculin
KeywordsCELL ADHESION / 5-Helix bundle / cytoskelatal protein / phospholipids / structural protein
Function / homology
Function and homology information


regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / beta-catenin binding / specific granule lumen / extracellular vesicle / 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 / Platelet degranulation / actin binding / secretory granule lumen / 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 / cytosol / cytoplasm
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: 2.76 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 1.2Oct 4, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vinculin
B: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2474
Polymers39,0632
Non-polymers1842
Water5,170287
1
A: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6242
Polymers19,5311
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6242
Polymers19,5311
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.153, 70.909, 118.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vinculin / / Metavinculin / MV


Mass: 19531.453 Da / Num. of mol.: 2 / Fragment: UNP Residues 959-1134 / Mutation: R975Q, K979Q, R1107Q, R1128Q
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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 20 mM citric acid, 80 mM Bis-Tris propane (pH 8.8), and 14 to 16% (w/v) PEG 3350

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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: Jul 23, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→60.79 Å / Num. obs: 10731 / % possible obs: 99.8 % / Redundancy: 9.6 % / Biso Wilson estimate: 40.61 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.022 / Net I/σ(I): 28.1
Reflection shellResolution: 2.76→2.91 Å / Redundancy: 9.1 % / Mean I/σ(I) obs: 13 / CC1/2: 0.995 / % possible all: 99.7

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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: 2.76→60.79 Å / Cor.coef. Fo:Fc: 0.9444 / Cor.coef. Fo:Fc free: 0.9199 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.381
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 526 4.92 %RANDOM
Rwork0.2014 ---
obs0.2038 10690 99.99 %-
Displacement parametersBiso mean: 26.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.2258 Å20 Å20 Å2
2---4.3258 Å20 Å2
3---5.5515 Å2
Refine analyzeLuzzati coordinate error obs: 0.265 Å
Refinement stepCycle: 1 / Resolution: 2.76→60.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 12 287 3038
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012777HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.073746HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1386SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes82HARMONIC2
X-RAY DIFFRACTIONt_gen_planes391HARMONIC5
X-RAY DIFFRACTIONt_it2777HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion396SEMIHARMONIC5
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_contact3408SEMIHARMONIC4
LS refinement shellResolution: 2.76→3.08 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3036 154 5.2 %
Rwork0.1684 2808 -
all0.1748 2962 -
obs--99.99 %

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