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- PDB-1tr2: Crystal structure of human full-length vinculin (residues 1-1066) -

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Basic information

Entry
Database: PDB / ID: 1tr2
TitleCrystal structure of human full-length vinculin (residues 1-1066)
ComponentsVINCULIN ISOFORM 1
KeywordsCELL ADHESION / ACTIN-BINDING
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 / maintenance of blood-brain barrier / regulation of focal adhesion assembly / 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 / extracellular vesicle / 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 / 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, Vh2 four-helix bundle / 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) ...Vinculin, Vh2 four-helix bundle / 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 / SAD / Resolution: 2.9 Å
AuthorsBorgon, R.A. / Vonrhein, C. / Bricogne, G. / Bois, P.R. / Izard, T.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of Human Vinculin
Authors: Borgon, R.A. / Vonrhein, C. / Bricogne, G. / Bois, P.R. / Izard, T.
History
DepositionJun 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: VINCULIN ISOFORM 1
B: VINCULIN ISOFORM 1


Theoretical massNumber of molelcules
Total (without water)237,1282
Polymers237,1282
Non-polymers00
Water3,927218
1
A: VINCULIN ISOFORM 1


Theoretical massNumber of molelcules
Total (without water)118,5641
Polymers118,5641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VINCULIN ISOFORM 1


Theoretical massNumber of molelcules
Total (without water)118,5641
Polymers118,5641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.740, 154.080, 108.950
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein VINCULIN ISOFORM 1


Mass: 118563.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Plasmid: PET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) and BL21(DE3) / References: UniProt: P18206
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 11

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.97 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97927
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.9→56.86 Å / Num. obs: 48752 / % possible obs: 100 % / Redundancy: 23.7 % / Biso Wilson estimate: 103.211 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 21
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
BUSTER-TNT1.1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→56.86 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME OF THE WATER MOLECULES ARE PLACED IN DISORDERED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.3005 2507 5.15 %RANDOM
Rwork0.2322 ---
obs0.2356 48752 100 %-
Displacement parametersBiso mean: 92.83 Å2
Baniso -1Baniso -2Baniso -3
1--13.42714954 Å20 Å2-0.9340888 Å2
2--3.12342373 Å20 Å2
3---10.30372581 Å2
Refine analyzeLuzzati coordinate error obs: 0.4897 Å
Refinement stepCycle: LAST / Resolution: 2.9→56.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15815 0 0 218 16033
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.006159882
X-RAY DIFFRACTIONt_angle_deg0.945214832
X-RAY DIFFRACTIONt_dihedral_angle_d20.42499670
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle24.07781
X-RAY DIFFRACTIONt_trig_c_planes0.0054972
X-RAY DIFFRACTIONt_gen_planes0.0122715
X-RAY DIFFRACTIONt_it1.7141596420
X-RAY DIFFRACTIONt_nbd0.0549715
LS refinement shellResolution: 2.9→3.07 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3356 423 5.47 %
Rwork0.2809 7304 -
all28.39 7727 -
obs--99.8 %

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