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- PDB-5l0c: Human metavinculin (residues 959-1134) in complex with PIP2 -

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Basic information

Entry
Database: PDB / ID: 5l0c
TitleHuman metavinculin (residues 959-1134) in complex with PIP2
ComponentsVinculin
KeywordsCELL ADHESION / 5-Helix bundle / cytoskelatal protein / lipids / 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 / 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
Chem-PIO / PHOSPHATE ION / Vinculin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _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
C: Vinculin
D: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,49712
Polymers78,4794
Non-polymers4,0188
Water1,09961
1
A: Vinculin
hetero molecules

C: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8275
Polymers39,2392
Non-polymers1,5883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
Buried area2010 Å2
ΔGint-16 kcal/mol
Surface area19610 Å2
MethodPISA
2
B: Vinculin
hetero molecules

D: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6697
Polymers39,2392
Non-polymers2,4305
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_656-x+3/2,y+1/2,-z+11
Buried area2490 Å2
ΔGint-11 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.520, 100.676, 105.615
Angle α, β, γ (deg.)90.00, 122.49, 90.00
Int Tables number5
Space group name H-MC121
DetailsDimer confirmed by FRET assay

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Components

#1: Protein
Vinculin / Metavinculin / MV


Mass: 19619.697 Da / Num. of mol.: 4 / Fragment: UNP Residues 959-1130
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-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C25H49O19P3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.28 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 20 mM citric acid, 80 mM Bis-Tris propane (pH 3.4), and 16% (w/v) PEG 3350
PH range: 3.4 - 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.1→89.08 Å / Num. obs: 18132 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 129.44 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.034 / Net I/σ(I): 15.2
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.742 / % possible all: 100

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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: 3.1→30.45 Å / Cor.coef. Fo:Fc: 0.9358 / Cor.coef. Fo:Fc free: 0.9337 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.439
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 922 5.1 %RANDOM
Rwork0.2354 ---
obs0.2368 18066 97.87 %-
Displacement parametersBiso mean: 115.97 Å2
Baniso -1Baniso -2Baniso -3
1--3.9187 Å20 Å27.0881 Å2
2--4.4942 Å20 Å2
3----0.5755 Å2
Refine analyzeLuzzati coordinate error obs: 0.955 Å
Refinement stepCycle: 1 / Resolution: 3.1→30.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5387 0 140 61 5588
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015577HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.137547HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2796SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes143HARMONIC2
X-RAY DIFFRACTIONt_gen_planes774HARMONIC5
X-RAY DIFFRACTIONt_it5577HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion3.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion807SEMIHARMONIC5
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_contact6397SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.29 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2785 146 4.9 %
Rwork0.2475 2833 -
all0.249 2979 -
obs--97.87 %

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