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- PDB-4pr9: Human Vinculin (residues 891-1066) in complex with PIP -

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Basic information

Entry
Database: PDB / ID: 4pr9
TitleHuman Vinculin (residues 891-1066) in complex with PIP
ComponentsVinculin
KeywordsCELL ADHESION / STRUCTURAL PROTEIN / 5-helix bundle / cytoskeletal protein / lipids
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 / terminal web / cell-substrate junction / 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 / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / 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 / cell-matrix adhesion / cell projection / morphogenesis of an epithelium / 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 / Signaling by BRAF and RAF1 fusions / cell-cell junction / extracellular vesicle / Signaling by ALK fusions and activated point mutants / 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 / 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 / MIR / Resolution: 3.2 Å
AuthorsChinthalapudi, K. / Rangarajan, E.S. / Patil, D. / Izard, T.
CitationJournal: To be Published
Title: Mechanism and function of lipid-directed oligomerization of vinculin
Authors: Chinthalapudi, K. / Rangarajan, E.S. / Patil, D. / Izard, T.
History
DepositionMar 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: Vinculin
F: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,55912
Polymers118,0436
Non-polymers2,5166
Water72140
1
A: Vinculin
B: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9335
Polymers39,3482
Non-polymers1,5853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Vinculin
D: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4403
Polymers39,3482
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Vinculin
F: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1864
Polymers39,3482
Non-polymers8392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.579, 102.579, 190.772
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein
Vinculin


Mass: 19673.855 Da / Num. of mol.: 6
Fragment: C-terminal domain (UNP residues 891-1066 of isoform 1)
Mutation: R1060A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid: pGEX 6P1 / Production host: Escherichia coli (E. coli) / 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.: 3 / Source method: obtained synthetically / Formula: C25H49O19P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG3350, 2% tryptone, 0.05 M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Aug 12, 2013
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: 3.2→88.836 Å / Num. all: 19218 / Num. obs: 19218 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 111.64 Å2 / Rmerge(I) obs: 0.053
Reflection shellResolution: 3.2→3.37 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
BUSTER2.11.4refinement
XDSdata reduction
autoPROCdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1RKE

1rke


Resolution: 3.2→45.17 Å / Cor.coef. Fo:Fc: 0.9543 / Cor.coef. Fo:Fc free: 0.9316 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.509 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 967 5.04 %RANDOM
Rwork0.2039 ---
obs0.2062 19178 99.68 %-
all-19218 --
Displacement parametersBiso mean: 142.05 Å2
Baniso -1Baniso -2Baniso -3
1-9.7218 Å20 Å20 Å2
2--9.7218 Å20 Å2
3----19.4437 Å2
Refine analyzeLuzzati coordinate error obs: 1.018 Å
Refinement stepCycle: LAST / Resolution: 3.2→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7994 0 140 40 8174
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018211HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1411033HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3179SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes209HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1153HARMONIC5
X-RAY DIFFRACTIONt_it8211HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion3.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1173SEMIHARMONIC5
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_contact9535SEMIHARMONIC4
LS refinement shellResolution: 3.2→3.37 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2632 144 5.26 %
Rwork0.234 2594 -
all0.2356 2738 -
obs--99.68 %

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