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- PDB-1t01: Vinculin complexed with the VBS1 helix from talin -

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Basic information

Entry
Database: PDB / ID: 1t01
TitleVinculin complexed with the VBS1 helix from talin
Components
  • Talin 1
  • unnamed protein product
KeywordsCELL ADHESION / STRUCTURAL PROTEIN / five helix bundle
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / GRB2:SOS provides linkage to MAPK signaling for Integrins / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / Integrin signaling / Smooth Muscle Contraction ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / GRB2:SOS provides linkage to MAPK signaling for Integrins / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / terminal web / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / Platelet degranulation / dystroglycan binding / muscle alpha-actinin binding / MAP2K and MAPK activation / alpha-catenin binding / vinculin binding / fascia adherens / cell-cell contact zone / integrin activation / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / cell-substrate junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / cortical actin cytoskeleton organization / regulation of focal adhesion assembly / phosphatidylserine binding / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / regulation of cell migration / ruffle / phosphatidylinositol binding / cell projection / Neutrophil degranulation / integrin-mediated signaling pathway / morphogenesis of an epithelium / adherens junction / neuromuscular junction / structural constituent of cytoskeleton / sarcolemma / beta-catenin binding / ruffle membrane / platelet aggregation / Z disc / cell-cell adhesion / cell-cell junction / actin filament binding / actin cytoskeleton / integrin binding / 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 / cytoplasm
Similarity search - Function
Vinculin repeated domain signature. / : / Talin, R4 domain / Vinculin / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment ...Vinculin repeated domain signature. / : / Talin, R4 domain / Vinculin / Alpha-catenin/vinculin-like / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Phosphotyrosine-binding domain / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsPapagrigoriou, E. / Gingras, A.R. / Barsukov, I.L. / Critchley, D.R. / Emsley, J.
CitationJournal: Embo J. / Year: 2004
Title: Activation of a vinculin-binding site in the talin rod involves rearrangement of a five-helix bundle
Authors: PAPAGRIGORIOU, E. / GINGRAS, A.R. / BARSUKOV, I.L. / Bate, N. / Fillingham, I.J. / Patel, B. / Frank, R. / Ziegler, W.H. / Roberts, G.C. / Critchley, D.R. / Emsley, J.
History
DepositionApr 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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: unnamed protein product
B: Talin 1


Theoretical massNumber of molelcules
Total (without water)30,9302
Polymers30,9302
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-26 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.645, 71.421, 96.093
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 unnamed protein product


Mass: 28523.053 Da / Num. of mol.: 1 / Fragment: vinculin head
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 (bacteria) / Strain (production host): BL21 / References: UniProt: P12003
#2: Protein/peptide Talin 1


Mass: 2406.803 Da / Num. of mol.: 1 / Fragment: talin (vinculin binding site 1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TLN1, TLN / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P26039
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.93 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 30%PEG 5000, 0.1M MES, 0.2M Ammonium Sulphate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.972
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 24132 / % possible obs: 98.4 % / Rsym value: 0.059
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 2.509 / Rsym value: 0.495 / % possible all: 90.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 2.06 Å
RfactorNum. reflectionSelection details
Rfree0.303 1069 RANDOM
Rwork0.23 --
obs-22582 -
Displacement parametersBiso mean: 49.92 Å2
Refinement stepCycle: LAST / Highest resolution: 2.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 0 311 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.4861.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it2.2912
X-RAY DIFFRACTIONc_scangle_it3.4442.5
LS refinement shellResolution: 2.06→2.15 Å / Rfactor Rfree error: 0.027
RfactorNum. reflection% reflection
Rfree0.3 127 -
Rwork0.306 --
obs--86.1 %

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