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- PDB-1xwj: Vinculin head (1-258) in complex with the talin vinculin binding ... -

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Basic information

Entry
Database: PDB / ID: 1xwj
TitleVinculin head (1-258) in complex with the talin vinculin binding site 3 (1945-1969)
Components
  • Talin
  • Vinculin
KeywordsCELL ADHESION/PROTEIN BINDING / Vinculin / Talin / CELL ADHESION-PROTEIN BINDING COMPLEX
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 / muscle alpha-actinin binding / dystroglycan binding / MAP2K and MAPK activation / alpha-catenin binding / fascia adherens / vinculin binding / cell-cell contact zone / apical junction assembly / costamere / adherens junction assembly / regulation of establishment of endothelial barrier / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / ruffle / regulation of cell migration / Neutrophil degranulation / cell projection / morphogenesis of an epithelium / adherens junction / neuromuscular junction / sarcolemma / structural constituent of cytoskeleton / cell-cell adhesion / ruffle membrane / Z disc / beta-catenin binding / actin filament binding / cell-cell junction / integrin binding / actin cytoskeleton / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / cell surface / protein homodimerization activity / protein-containing complex / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / : ...Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin IBS2B domain / Talin, N-terminal F0 domain / N-terminal or F0 domain of Talin-head FERM / Vinculin, conserved site / Vinculin family talin-binding region signature. / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Vinculin/alpha-catenin / Vinculin family / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Four Helix Bundle (Hemerythrin (Met), subunit A) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vinculin / Talin-1 / Talin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsGingras, A.R. / Papagrigoriou, E. / Barsukov, I.L. / Critchley, D.R. / Emsley, J.
CitationJournal: Biochemistry / Year: 2006
Title: Structural and Dynamic Characterization of a Vinculin Binding Site in the Talin Rod
Authors: Gingras, A.R. / Vogel, K.P. / Steinhoff, H.J. / Ziegler, W.H. / Patel, B. / Emsley, J. / Critchley, D.R. / Roberts, G.C. / Barsukov, I.L.
History
DepositionNov 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: Vinculin
B: Talin


Theoretical massNumber of molelcules
Total (without water)34,2322
Polymers34,2322
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-23 kcal/mol
Surface area14150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.173, 72.434, 96.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Vinculin / Metavinculin


Mass: 31327.104 Da / Num. of mol.: 1 / Fragment: residues -21-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P12003
#2: Protein/peptide Talin


Mass: 2905.392 Da / Num. of mol.: 1 / Fragment: residues 1945-1970 / Source method: obtained synthetically / Details: This sequence occurs naturally in chicken talin / References: UniProt: Q8AWI0, UniProt: P54939*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M NaH2PO4, 1M K2HPO4, 0.1M CAPS, pH 10.9, 3% Hexanediol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979625, 0.972447, 0.979404
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 23, 2004 / Details: Zeiss mirror
RadiationMonochromator: Khozu monochromator (i.e. Si(111)) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9796251
20.9724471
30.9794041
ReflectionResolution: 2.6→30 Å / Num. all: 99069 / Num. obs: 11765 / % possible obs: 92.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.099
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.211 / % possible all: 78.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→28.95 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 552 5 %RANDOM
Rwork0.241 ---
all-10568 --
obs--89.9 %-
Refinement stepCycle: LAST / Resolution: 2.6→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2098 0 0 46 2144
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.037
RfactorNum. reflection% reflection
Rfree0.316 73 -
Rwork0.271 --
obs-1429 78.8 %

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