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- PDB-1qkr: Crystal structure of the vinculin tail and a pathway for activation -

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Basic information

Entry
Database: PDB / ID: 1qkr
TitleCrystal structure of the vinculin tail and a pathway for activation
ComponentsVINCULIN
KeywordsACTIN CYTOSKELETON / CELL ADHESION / HELICAL BUNDLE / LIPID BINDING
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / MAP2K and MAPK activation / muscle alpha-actinin binding / alpha-catenin binding / fascia adherens / vinculin binding / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / regulation of cell migration / Neutrophil degranulation / morphogenesis of an epithelium / cell projection / adherens junction / neuromuscular junction / sarcolemma / beta-catenin binding / Z disc / actin filament binding / cell-cell junction / actin cytoskeleton / scaffold protein binding / cytoskeleton / mitochondrial inner membrane / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / protein homodimerization activity / protein-containing complex / plasma membrane / 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 speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsBakolitsa, C. / De Pereda, J.M. / Bagshaw, C.R. / Critchley, D.R. / Liddington, R.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal Structure of the Vinculin Tail and a Pathway for Activation
Authors: Bakolitsa, C. / De Pereda, J.M. / Bagshaw, C.R. / Critchley, D.R. / Liddington, R.C.
History
DepositionAug 4, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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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)43,4514
Polymers43,2592
Non-polymers1922
Water5,693316
1
A: VINCULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7262
Polymers21,6291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: VINCULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7262
Polymers21,6291
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)39.600, 87.770, 50.630
Angle α, β, γ (deg.)90.00, 91.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VINCULIN / TAIL DOMAIN


Mass: 21629.486 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GALLUS GALLUS (chicken) / Tissue: MUSCLE / Gene: VCL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12003
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 44 %
Crystal growpH: 5
Details: 25% (W/V) PEG 2000, 0.2 M (NH4)2SO4, 0.1 M CH3COO PH 5.0
Crystal
*PLUS
Density % sol: 44 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
2150 mM1dropNaCl
320 mMTris1drop
44 mMdithiothreitol1drop
525 %(w/v)PEG20001reservoir
60.2 Mammonium sulfate1reservoir
70.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→10 Å / Num. obs: 30415 / % possible obs: 95.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.064 / Net I/σ(I): 16.6
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.27 / % possible all: 88.3
Reflection
*PLUS
Lowest resolution: 25 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
SOLVEphasing
CNS0.5refinement
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→10 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1508 5 %RANDOM
Rwork0.2 ---
obs0.2 30415 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.2752 Å2 / ksol: 0.426906 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å20 Å2-3.27 Å2
2--5.39 Å20 Å2
3----1.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-10 Å
Luzzati sigma a0.12 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 10 316 3131
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it3.142
X-RAY DIFFRACTIONc_scbond_it4.472
X-RAY DIFFRACTIONc_scangle_it6.962.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 226 4.9 %
Rwork0.244 4422 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rfree: 0.28

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