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- PDB-3s90: Human vinculin head domain Vh1 (residues 1-252) in complex with m... -

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Basic information

Entry
Database: PDB / ID: 3s90
TitleHuman vinculin head domain Vh1 (residues 1-252) in complex with murine talin (VBS33; residues 1512-1546)
Components
  • Talin-1
  • Vinculin
KeywordsCELL ADHESION / four-helix bundle / focal adhesion
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 / 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 / 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 / Smooth Muscle Contraction / MAP2K and MAPK activation / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / Platelet degranulation / dystroglycan binding / cortical microtubule organization / alpha-catenin binding / fascia adherens / vinculin binding / cell-cell contact zone / integrin activation / apical junction assembly / costamere / adherens junction assembly / 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 / maintenance of blood-brain barrier / phosphatidylserine binding / brush border / Smooth Muscle Contraction / ruffle / cell-matrix adhesion / phosphatidylinositol binding / negative regulation of cell migration / cell projection / integrin-mediated signaling pathway / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / structural constituent of cytoskeleton / platelet aggregation / beta-catenin binding / cell-cell adhesion / 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 / Signaling by BRAF and RAF1 fusions / actin filament binding / cell-cell junction / Signaling by ALK fusions and activated point mutants / extracellular vesicle / integrin binding / Platelet degranulation / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / molecular adaptor activity / 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)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsYogesha, S.D. / Sharff, A. / Bricogne, G. / Izard, T.
CitationJournal: Protein Sci. / Year: 2011
Title: Intermolecular versus intramolecular interactions of the vinculin binding site 33 of talin.
Authors: Yogesha, S.D. / Sharff, A. / Bricogne, G. / Izard, T.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Dec 19, 2012Group: Database references
Revision 1.4Oct 29, 2014Group: Structure summary
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Revision 1.6Sep 13, 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 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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: Vinculin
C: Talin-1
D: Talin-1


Theoretical massNumber of molelcules
Total (without water)64,7394
Polymers64,7394
Non-polymers00
Water7,314406
1
A: Vinculin
C: Talin-1


Theoretical massNumber of molelcules
Total (without water)32,3692
Polymers32,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-28 kcal/mol
Surface area14710 Å2
MethodPISA
2
B: Vinculin
D: Talin-1


Theoretical massNumber of molelcules
Total (without water)32,3692
Polymers32,3692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-26 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.830, 61.180, 71.420
Angle α, β, γ (deg.)83.27, 79.05, 69.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Vinculin / Metavinculin


Mass: 28265.807 Da / Num. of mol.: 2 / Fragment: unp residues 1-252
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Escherichia coli (E. coli) / References: UniProt: P18206
#2: Protein/peptide Talin-1


Mass: 4103.681 Da / Num. of mol.: 2 / Fragment: unp residues 1512-1546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Production host: Escherichia coli (E. coli) / References: UniProt: P26039
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1 M citrate 5.3, 15% (w/v) PEG 10K, 1.5% (v/v) dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→70.01 Å / Num. all: 51772 / Num. obs: 51772 / % possible obs: 96.7 % / Redundancy: 2.8 % / Biso Wilson estimate: 30.76 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 14.2
Reflection shellResolution: 1.973→1.98 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.3 / Num. unique all: 510 / Rsym value: 0.533 / % possible all: 95.9

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
BUSTER2.13.0refinement
autoPROCdata scaling
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2IBF

2ibf


Resolution: 1.97→70.01 Å / Cor.coef. Fo:Fc: 0.9504 / Cor.coef. Fo:Fc free: 0.9405 / SU R Cruickshank DPI: 0.14 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2096 2625 5.07 %RANDOM
Rwork0.1863 ---
all0.1874 ---
obs0.1874 51740 96.24 %-
Displacement parametersBiso mean: 51.11 Å2
Refine analyzeLuzzati coordinate error obs: 0.324 Å
Refinement stepCycle: LAST / Resolution: 1.97→70.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 0 406 4694
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014333HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975856HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2130SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes602HARMONIC5
X-RAY DIFFRACTIONt_it4333HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion2.89
X-RAY DIFFRACTIONt_chiral_improper_torsion616SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5644SEMIHARMONIC4
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2331 159 4.48 %
Rwork0.2181 3388 -
all0.2187 3547 -
obs-3547 96.24 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.35430.75693.0720.19550.5952.11970.140.56520.1374-0.0075-0.1288-0.02460.12680.0588-0.0113-0.21190.0940.010.2187-0.1302-0.228247.617123.68340.2706
24.15023.5490.1173.13130.13090.17810.04930.1566-0.04940.1347-0.00180.14170.00050.0022-0.0475-0.10480.04690.0145-0.1529-0.07770.123961.38643.309170.4037
32.7388-2.972-3.26952.4248-0.2731.85550.03650.0917-0.26590.0911-0.1601-0.29170.0761-0.02840.1236-0.02680.1778-0.16230.1611-0.1344-0.20533.80929.783932.2293
43.3684-0.95412.55960.0409-1.53433.7059-0.0455-0.3069-0.06680.16580.1491-0.0456-0.02530.1038-0.1036-0.0646-0.03740.0707-0.0713-0.1650.063348.1408-8.133580.7742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 388
2X-RAY DIFFRACTION2{ B|* }B2 - 388
3X-RAY DIFFRACTION3{ C|* }C1520 - 1546
4X-RAY DIFFRACTION4{ D|* }D1520 - 1545

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