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- PDB-1syq: Human vinculin head domain VH1, residues 1-258, in complex with h... -

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Basic information

Entry
Database: PDB / ID: 1syq
TitleHuman vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin binding site 1, residues 607-636
Components
  • Talin 1
  • vinculin isoform VCL
KeywordsCELL ADHESION / cytoskeleton / vinculin / talin
Function / homology
Function and homology information


regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / dystroglycan binding ...regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / dystroglycan binding / alpha-catenin binding / cortical microtubule organization / fascia adherens / XBP1(S) activates chaperone genes / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cell-cell contact zone / vinculin binding / integrin activation / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / cell-substrate junction assembly / cell-cell junction assembly / axon extension / protein localization to cell surface / cortical actin cytoskeleton organization / lamellipodium assembly / regulation of focal adhesion assembly / p130Cas linkage to MAPK signaling for integrins / phosphatidylserine binding / maintenance of blood-brain barrier / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / Smooth Muscle Contraction / ruffle / Integrin signaling / phosphatidylinositol binding / negative regulation of cell migration / cell-matrix adhesion / cell projection / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / morphogenesis of an epithelium / integrin-mediated signaling pathway / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / cell-cell adhesion / structural constituent of cytoskeleton / platelet aggregation / ruffle membrane / specific granule lumen / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin filament binding / Signaling by BRAF and RAF1 fusions / integrin binding / Signaling by ALK fusions and activated point mutants / cell-cell junction / extracellular vesicle / Platelet degranulation / actin binding / actin cytoskeleton organization / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / secretory granule lumen / molecular adaptor activity / ficolin-1-rich granule lumen / cytoskeleton / cell adhesion / cadherin binding / membrane raft / focal adhesion / ubiquitin protein ligase binding / Neutrophil degranulation / structural molecule activity / cell surface / protein-containing complex / extracellular exosome / extracellular region / 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 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsIzard, T. / Vonrhein, C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural basis for amplifying vinculin activation by talin
Authors: Izard, T. / Vonrhein, C.
History
DepositionApr 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 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

Downloads & links

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Assembly

Deposited unit
A: vinculin isoform VCL
B: Talin 1


Theoretical massNumber of molelcules
Total (without water)32,1882
Polymers32,1882
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-29 kcal/mol
Surface area14700 Å2
MethodPISA
2
A: vinculin isoform VCL
B: Talin 1
x 6


Theoretical massNumber of molelcules
Total (without water)193,12812
Polymers193,12812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area29200 Å2
ΔGint-213 kcal/mol
Surface area72890 Å2
MethodPISA
3
A: vinculin isoform VCL
B: Talin 1
x 6


Theoretical massNumber of molelcules
Total (without water)193,12812
Polymers193,12812
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_544y+1/3,x-1/3,-z-1/31
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
crystal symmetry operation18_654-x+4/3,-x+y+2/3,-z-1/31
Buried area31080 Å2
ΔGint-216 kcal/mol
Surface area71010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.098, 141.098, 104.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein vinculin isoform VCL


Mass: 29766.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: peT3d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P18206
#2: Protein/peptide Talin 1


Mass: 2421.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / References: UniProt: Q9Y490
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.12 Å3/Da / Density % sol: 60.59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97889
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. obs: 15061 / % possible obs: 97.6 % / Redundancy: 18 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.179 / Net I/σ(I): 8.3
Reflection shellResolution: 2.42→2.51 Å / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3 / % possible all: 80.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→32.25 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2709941.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 774 5.1 %RANDOM
Rwork0.188 ---
all0.188 ---
obs0.194 15060 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5471 Å2 / ksol: 0.322653 e/Å3
Displacement parametersBiso mean: 56.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å23.85 Å20 Å2
2--4.25 Å20 Å2
3----8.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.42→32.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 0 190 2389
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.751.5
X-RAY DIFFRACTIONc_mcangle_it5.262
X-RAY DIFFRACTIONc_scbond_it11.672
X-RAY DIFFRACTIONc_scangle_it14.962.5
LS refinement shellResolution: 2.42→2.57 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.258 118 5.4 %
Rwork0.226 2071 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER-TOPOLOGY
X-RAY DIFFRACTION4ION.PARAMION.TOP

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