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- PDB-1zw3: Vinculin Head (0-258) in Complex with the Talin Rod residues 1630-1652 -

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Basic information

Entry
Database: PDB / ID: 1zw3
TitleVinculin Head (0-258) in Complex with the Talin Rod residues 1630-1652
Components
  • Talin 1
  • Vinculin
KeywordsPROTEIN BINDING / TALIN / VINCULIN / 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 / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling ...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 / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / Smooth Muscle Contraction / fascia adherens / MAP2K and MAPK activation / Platelet degranulation / dystroglycan binding / muscle alpha-actinin binding / alpha-catenin binding / cortical microtubule organization / vinculin binding / cell-cell contact zone / integrin activation / apical junction assembly / costamere / regulation of establishment of endothelial barrier / cell-substrate junction assembly / axon extension / adherens junction assembly / protein localization to cell surface / cortical actin cytoskeleton organization / lamellipodium assembly / regulation of focal adhesion assembly / phosphatidylserine binding / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / ruffle / phosphatidylinositol binding / regulation of cell migration / Neutrophil degranulation / morphogenesis of an epithelium / integrin-mediated signaling pathway / cell projection / adherens junction / neuromuscular junction / sarcolemma / beta-catenin binding / structural constituent of cytoskeleton / ruffle membrane / integrin 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 / cell surface / protein homodimerization activity / protein-containing complex / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Talin VBS2 domain / 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 / Talin VBS2 domain / 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, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGingras, A.R. / Ziegler, W.H. / Barsukov, I.L. / Roberts, G.C. / Critchley, D.R. / Emsley, J.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Mapping and consensus sequence identification for multiple vinculin binding sites within the talin rod
Authors: Gingras, A.R. / Ziegler, W.H. / Frank, R. / Barsukov, I.L. / Roberts, G.C. / Critchley, D.R. / Emsley, J.
History
DepositionJun 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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 1


Theoretical massNumber of molelcules
Total (without water)34,0282
Polymers34,0282
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-22 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.621, 72.168, 96.725
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: 31195.908 Da / Num. of mol.: 1 / Fragment: Residues 0-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL, VINC1 / 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 1


Mass: 2832.331 Da / Num. of mol.: 1 / Fragment: Residues 1630-1652 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Mus musculus (Mouse).
References: UniProt: P26039

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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: 2.7 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 1.2M NaH2PO4/0.8M K2HPO4, 100mM CAPS, pH 10.5, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2004 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 5837 / % possible obs: 99.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.85
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.03 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XWJ

1xwj


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.853 / SU B: 24.832 / SU ML: 0.431 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.64 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30723 265 4.6 %RANDOM
Rwork0.22446 ---
obs0.22808 5533 99.9 %-
all-5837 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.771 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2--5.02 Å20 Å2
3----3.99 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2136 0 0 0 2136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222161
X-RAY DIFFRACTIONr_bond_other_d0.0020.022081
X-RAY DIFFRACTIONr_angle_refined_deg2.2861.982921
X-RAY DIFFRACTIONr_angle_other_deg1.08534849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4375272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59724.88486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.17915424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8361514
X-RAY DIFFRACTIONr_chiral_restr0.2040.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02376
X-RAY DIFFRACTIONr_nbd_refined0.2980.2748
X-RAY DIFFRACTIONr_nbd_other0.2080.22381
X-RAY DIFFRACTIONr_nbtor_refined0.2190.21129
X-RAY DIFFRACTIONr_nbtor_other0.1060.21469
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0050.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1361.51680
X-RAY DIFFRACTIONr_mcbond_other0.1511.5553
X-RAY DIFFRACTIONr_mcangle_it1.45122236
X-RAY DIFFRACTIONr_scbond_it1.9083883
X-RAY DIFFRACTIONr_scangle_it2.914.5685
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 16 -
Rwork0.223 398 -
obs--100 %

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