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- PDB-4dj9: Human vinculin head domain Vh1 (residues 1-258) in complex with t... -

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Basic information

Entry
Database: PDB / ID: 4dj9
TitleHuman vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin binding site 50 (VBS50, residues 2078-2099)
Components
  • Talin-1
  • Vinculin
KeywordsCELL ADHESION / cytoskeleton / focal adhesion / protein-protein interaction / four-helix bundle / F-actin / cytosol
Function / homology
Function and homology information


regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / dystroglycan binding ...regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / cell-substrate junction / terminal web / epithelial cell-cell adhesion / zonula adherens / LIM domain binding / dystroglycan binding / vinculin binding / alpha-catenin binding / XBP1(S) activates chaperone genes / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / fascia adherens / integrin activation / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / cell-substrate junction assembly / adherens junction assembly / axon extension / protein localization to cell surface / cell-cell junction assembly / lamellipodium assembly / cortical actin cytoskeleton organization / regulation of focal adhesion assembly / maintenance of blood-brain barrier / phosphatidylserine binding / p130Cas linkage to MAPK signaling for integrins / brush border / GRB2:SOS provides linkage to MAPK signaling for Integrins / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / ruffle / phosphatidylinositol binding / Integrin signaling / cell-matrix adhesion / negative regulation of cell migration / cell projection / integrin-mediated signaling pathway / morphogenesis of an epithelium / adherens junction / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / structural constituent of cytoskeleton / cell-cell adhesion / platelet aggregation / ruffle membrane / beta-catenin binding / specific granule lumen / Signaling by RAF1 mutants / extracellular vesicle / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / actin filament binding / cell-cell junction / Signaling by BRAF and RAF1 fusions / 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
: / Talin, R4 domain / 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 ...: / Talin, R4 domain / 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 / Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / 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. / Phosphotyrosine-binding domain / Vinculin/alpha-catenin / Vinculin family / 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: 2.25 Å
AuthorsYogesha, S.D. / Rangarajan, E.S. / Vonrhein, C. / Bricogne, G. / Izard, T.
CitationJournal: Protein Sci. / Year: 2012
Title: Crystal structure of vinculin in complex with vinculin binding site 50 (VBS50), the integrin binding site 2 (IBS2) of talin.
Authors: Yogesha, S.D. / Rangarajan, E.S. / Vonrhein, C. / Bricogne, G. / Izard, T.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1May 16, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vinculin
B: Talin-1


Theoretical massNumber of molelcules
Total (without water)31,8082
Polymers31,8082
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-27 kcal/mol
Surface area14130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.540, 68.160, 137.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vinculin / / Metavinculin


Mass: 28937.398 Da / Num. of mol.: 1 / Fragment: unp residues 1-258
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / References: UniProt: P18206
#2: Protein/peptide Talin-1


Mass: 2870.322 Da / Num. of mol.: 1 / Fragment: unp residues 2075-2103
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLN1, KIAA1027, TLN / References: UniProt: Q9Y490
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: The human vinculin Vh1 domain (residues 1 - 258) was generated as described.9 Crystallization screens of Vh1 protein and VBS50 mixed in 1:5 molar ratio were performed at two temperatures. Co- ...Details: The human vinculin Vh1 domain (residues 1 - 258) was generated as described.9 Crystallization screens of Vh1 protein and VBS50 mixed in 1:5 molar ratio were performed at two temperatures. Co-crystals were obtained from Hampton crystal screen I with a reservoir of 0.1 M Hepes pH 7.5, 10% w/v polyethylene glycol 6,000, and 5% 2-Methyl-2,4-pentanediol. Crystals were transferred directly from the initial 96-well screening plate into Paratone-N oil and flash-frozen in liquid nitrogen. , VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.25→68.8 Å / Num. obs: 15637 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 55.65 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 16.4
Reflection shellResolution: 2.251→2.258 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.592 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.13.0refinement
autoPROCdata scaling
XDS(VERSION December 6data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→68.8 Å / Cor.coef. Fo:Fc: 0.9429 / Cor.coef. Fo:Fc free: 0.9345 / SU R Cruickshank DPI: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 787 5.05 %RANDOM
Rwork0.2076 ---
obs0.2095 15586 99.32 %-
Displacement parametersBiso mean: 70.73 Å2
Baniso -1Baniso -2Baniso -3
1--15.5041 Å20 Å20 Å2
2---3.5916 Å20 Å2
3---19.0957 Å2
Refine analyzeLuzzati coordinate error obs: 0.349 Å
Refinement stepCycle: LAST / Resolution: 2.25→68.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 0 62 2079
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012066HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.122803HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d733SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes291HARMONIC5
X-RAY DIFFRACTIONt_it2066HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.15
X-RAY DIFFRACTIONt_other_torsion17.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion298SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2482SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3231 147 5.31 %
Rwork0.2344 2619 -
all0.2389 2766 -
obs--99.32 %
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)
10.98330.5986-0.71741.3344-2.02954.252-0.0831-0.00090.0481-0.3024-0.0765-0.01490.39330.12010.1596-0.22680.0757-0.0395-0.342-0.0573-0.319622.642818.0615-32.4915
22.78451.67970.86754.0065-2.9371.0852-0.0402-0.0037-0.2562-0.17880.09890.14690.1936-0.2419-0.0587-0.05710.0484-0.0161-0.10170.031-0.158821.419627.747-51.0589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|3 - A|254 }A3 - 254
2X-RAY DIFFRACTION2{ B|2078 - B|2099 }B2078 - 2099

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