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- PDB-1rke: Human vinculin head (1-258) in complex with human vinculin tail (... -

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Basic information

Entry
Database: PDB / ID: 1rke
TitleHuman vinculin head (1-258) in complex with human vinculin tail (879-1066)
Components
  • VCL protein
  • Vinculin
Keywordscell adhesion / structural protein / cytoskeleton / actin-binding / x-ray crystallography
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 / dystroglycan binding / alpha-catenin 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 / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / costamere / apical junction assembly / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Signaling by ALK fusions and activated point mutants / Smooth Muscle Contraction / cell-matrix adhesion / negative regulation of cell migration / cell projection / morphogenesis of an epithelium / adherens junction / sarcolemma / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / 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 / cell-cell junction / Signaling by BRAF and RAF1 fusions / 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 / protein-containing complex / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Vinculin repeated domain signature. / Vinculin / Alpha-catenin/vinculin-like / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.35 Å
AuthorsIzard, T. / Evans, G. / Borgon, R.A. / Rush, C.L. / Bricogne, G. / Bois, P.R.
CitationJournal: Nature / Year: 2004
Title: Vinculin activation by talin through helical bundle conversion
Authors: Izard, T. / Evans, G. / Borgon, R.A. / Rush, C.L. / Bricogne, G. / Bois, P.R.
History
DepositionNov 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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: Vinculin
B: VCL protein


Theoretical massNumber of molelcules
Total (without water)50,3252
Polymers50,3252
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-13 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.603, 161.648, 36.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein Vinculin /


Mass: 29489.982 Da / Num. of mol.: 1 / Fragment: vinculin head (residues 1-258)
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 VCL protein


Mass: 20835.076 Da / Num. of mol.: 1 / Fragment: vinculin tail (residues 879-1066)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P18206
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / pH: 8
Details: 15% PEG 3350; 50 mM NaCl; 100 mM Tris (pH 8); 10 mM DTT, pH 8.0, temperature 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %PEG33501reservoir
250 mM1reservoirNaCl
3100 mMTris1reservoirpH8
410 mMdithiothreitol1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9797 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.35→99.8 Å / Num. all: 21798 / Num. obs: 21798 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.5 Å2

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Processing

Software
NameVersionClassification
d*TREKdata scaling
SCALAdata scaling
SHARPphasing
BUSTER-TNTrefinement
d*TREKdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.35→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1118 5.1 %RANDOM
Rwork0.206 ---
all-21798 --
obs-21798 99.8 %-
Displacement parametersBiso mean: 56.2 Å2
Baniso -1Baniso -2Baniso -3
1-13 Å20 Å20 Å2
2---5.4 Å20 Å2
3----7.6 Å2
Refinement stepCycle: LAST / Resolution: 2.35→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 0 204 3660
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_angle_deg0.979
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
LS refinement shellResolution: 2.35→2.42 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.205 / Total num. of bins used: 9
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection all: 20680 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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