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- PDB-1st6: Crystal structure of a cytoskeletal protein -

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Basic information

Entry
Database: PDB / ID: 1st6
TitleCrystal structure of a cytoskeletal protein
ComponentsVinculin
KeywordsCELL ADHESION / up-down bundles
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / vinculin binding / muscle alpha-actinin binding / MAP2K and MAPK activation / 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 / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / regulation of cell migration / cell projection / Neutrophil degranulation / morphogenesis of an epithelium / adherens junction / sarcolemma / neuromuscular junction / Z disc / beta-catenin binding / actin filament binding / cell-cell junction / actin cytoskeleton / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / 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, Vh2 four-helix bundle / 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) ...Vinculin, Vh2 four-helix bundle / 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 / MAD / Resolution: 3.1 Å
AuthorsBakolitsa, C. / Liddington, R.C.
CitationJournal: Nature / Year: 2004
Title: Structural basis for vinculin activation at sites of cell adhesion.
Authors: Bakolitsa, C. / Cohen, D.M. / Bankston, L.A. / Bobkov, A.A. / Cadwell, G.W. / Jennings, L. / Critchley, D.R. / Craig, S.W. / Liddington, R.C.
History
DepositionMar 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vinculin


Theoretical massNumber of molelcules
Total (without water)117,5091
Polymers117,5091
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.020, 126.947, 351.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Vinculin / / Metavinculin


Mass: 117509.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12003

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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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulphate, cacodylic acid, dtt, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.93924, 0.97955
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 7, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.939241
20.979551
ReflectionResolution: 3.1→46.96 Å / Num. all: 23402 / Num. obs: 23379 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 99.6 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.1
Reflection shellResolution: 3.1→3.29 Å / Num. unique all: 3829 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
XPREPdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→46.96 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 3235608.91 / Data cutoff high rms absF: 3235608.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.357 1134 4.9 %RANDOM
Rwork0.316 ---
all0.318 23402 --
obs0.316 23379 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.3653 Å2 / ksol: 0.300822 e/Å3
Displacement parametersBiso mean: 127.5 Å2
Baniso -1Baniso -2Baniso -3
1-30.52 Å20 Å20 Å2
2---19.36 Å20 Å2
3----11.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.75 Å0.66 Å
Luzzati d res low-5 Å
Luzzati sigma a0.98 Å0.98 Å
Refinement stepCycle: LAST / Resolution: 3.1→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8058 0 0 0 8058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d2.23
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.427 190 5 %
Rwork0.428 3639 -
obs-3639 99.7 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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