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- PDB-6fuy: Crystal structure of human full-length vinculin-T12-A974K (residu... -

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Basic information

Entry
Database: PDB / ID: 6fuy
TitleCrystal structure of human full-length vinculin-T12-A974K (residues 1-1066)
ComponentsVinculin
KeywordsCELL ADHESION / Mechanosensitive Self-inhibition Adapter
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 / Vinculin, conserved site / Vinculin family talin-binding region signature. / Vinculin/alpha-catenin / Vinculin family / Alpha-catenin/vinculin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsChorev, D.S. / Volberg, T. / Livne, A. / Eisenstein, M. / Martins, B. / Kam, Z. / Jockusch, B.M. / Medalia, O. / Sharon, M. / Geiger, B.
Funding support Israel, 3items
OrganizationGrant numberCountry
ERC294852 Israel
ERC636752 Israel
ISF3001/13 Israel
CitationJournal: Sci Rep / Year: 2018
Title: Conformational states during vinculin unlocking differentially regulate focal adhesion properties.
Authors: Chorev, D.S. / Volberg, T. / Livne, A. / Eisenstein, M. / Martins, B. / Kam, Z. / Jockusch, B.M. / Medalia, O. / Sharon, M. / Geiger, B.
History
DepositionFeb 28, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionMar 14, 2018ID: 6FMM
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6992
Polymers116,6591
Non-polymers401
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Comparable structure to PDB 1TR2
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-6 kcal/mol
Surface area47670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.810, 97.810, 233.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Vinculin / / Metavinculin / MV


Mass: 116659.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VCL / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P18206
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.77 Å3/Da / Density % sol: 55.55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, calcium acetate, Tris-HOAc, 15% ethylene glycol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→19.91 Å / Num. obs: 26203 / % possible obs: 97.89 % / Redundancy: 19.85 % / Net I/σ(I): 24.68
Reflection shellResolution: 3→19.91 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TR2

1tr2


Resolution: 3→19.91 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.38
RfactorNum. reflection% reflection
Rfree0.3048 1311 5 %
Rwork0.265 --
obs0.2669 26202 98.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7350 0 1 5 7356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027445
X-RAY DIFFRACTIONf_angle_d0.55810039
X-RAY DIFFRACTIONf_dihedral_angle_d13.8284692
X-RAY DIFFRACTIONf_chiral_restr0.0351179
X-RAY DIFFRACTIONf_plane_restr0.0041312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.11980.39051460.3582762X-RAY DIFFRACTION100
3.1198-3.26120.38171470.33552797X-RAY DIFFRACTION100
3.2612-3.43230.39611440.32732732X-RAY DIFFRACTION100
3.4323-3.64610.39591350.35632568X-RAY DIFFRACTION92
3.6461-3.92560.43241370.34612606X-RAY DIFFRACTION93
3.9256-4.3170.27921470.25632785X-RAY DIFFRACTION100
4.317-4.93340.23291470.22392803X-RAY DIFFRACTION100
4.9334-6.18450.34241510.28542864X-RAY DIFFRACTION100
6.1845-19.91020.24671570.20992974X-RAY DIFFRACTION100
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)
10.07720.1251-0.10360.4752-0.1390.4808-0.36080.55770.04340.20550.3361-0.3710.17070.1124-0.07970.2721-0.19220.00171.0571-0.30020.735534.5207-35.87-20.5451
21.4026-0.37460.27390.48480.09010.86140.0740.4169-0.1818-0.18050.2852-0.0294-0.314-0.23790.02120.2861-0.03860.06370.4671-0.0160.48477.1135-40.7225-18.3809
30.61780.67640.09530.6632-0.05480.00610.1767-0.1970.20970.4048-0.24150.2004-0.3057-0.1204-0.00011.0163-0.0565-0.09941.0893-0.0430.85415.4872-9.5499-7.3348
40.61820.03980.16610.4504-0.3111.6339-0.08550.05040.0180.22670.066-0.0387-0.12610.0457-00.5212-0.07350.0710.4959-0.0830.52628.8129-23.471913.231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 918 through 1066 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 249 )
3X-RAY DIFFRACTION3chain 'A' and (resid 250 through 512 )
4X-RAY DIFFRACTION4chain 'A' and (resid 513 through 917 )

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