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- PDB-6nr7: Rerefinement of chicken vinculin -

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Basic information

Entry
Database: PDB / ID: 6nr7
TitleRerefinement of chicken vinculin
ComponentsVinculin
KeywordsCELL ADHESION / focal adhesions / cytoskeleton interaction / cell spreading / force transmission
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / MAP2K and MAPK activation / muscle alpha-actinin binding / alpha-catenin binding / fascia adherens / vinculin binding / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / adherens junction assembly / axon extension / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / regulation of cell migration / Neutrophil degranulation / morphogenesis of an epithelium / cell projection / adherens junction / neuromuscular junction / sarcolemma / beta-catenin binding / Z disc / actin filament binding / cell-cell junction / actin cytoskeleton / scaffold protein binding / cytoskeleton / mitochondrial inner membrane / cell adhesion / cadherin binding / focal adhesion / ubiquitin protein ligase binding / structural molecule activity / protein homodimerization activity / protein-containing complex / plasma membrane / 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
Chem-KYG / PHOSPHATE ION / Vinculin
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsStec, B.
CitationJournal: To be published
Title: Refined model of chicken vinculin suggests the mechanism of activation by helical super-bundle unfurling
Authors: Stec, D.L. / Stec, B.
History
DepositionJan 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vinculin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,2046
Polymers119,3271
Non-polymers8765
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.020, 126.947, 351.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Vinculin / Metavinculin


Mass: 119327.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL, VINC1 / Production host: Escherichia coli (E. coli) / References: UniProt: P12003
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-KYG / (1R,2R,3S,4R,5R,6S)-4-{[(S)-[(2S)-2,3-dihydroxypropoxy](hydroxy)phosphoryl]oxy}-3,5,6-trihydroxycyclohexane-1,2-diyl bis[dihydrogen (phosphate)]


Mass: 494.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H21O17P3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 303 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: ammonium sulphate, cacodylic acid, dtt, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97955 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 2.99→46.96 Å / Num. obs: 25853 / % possible obs: 99 % / Observed criterion σ(F): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 98.2 Å2 / Rmerge(I) obs: 0.092 / Net I/av σ(I): 17.1 / Net I/σ(I): 17.1
Reflection shellResolution: 2.99→3.1 Å / Num. unique obs: 2481

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1st6

1st6


Resolution: 3→46.96 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.911 / SU B: 71.95 / SU ML: 0.582 / Cross valid method: THROUGHOUT / ESU R Free: 0.562 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31466 1134 4.4 %RANDOM
Rwork0.21913 ---
obs0.22382 24589 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 113.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.59 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 3→46.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 49 58 8443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138496
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178129
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.65211486
X-RAY DIFFRACTIONr_angle_other_deg1.2091.58118921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.08751085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.02322.54441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.858151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2461569
X-RAY DIFFRACTIONr_chiral_restr0.0680.21157
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029456
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021579
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2199.8154343
X-RAY DIFFRACTIONr_mcbond_other5.2169.8154342
X-RAY DIFFRACTIONr_mcangle_it8.50814.7195427
X-RAY DIFFRACTIONr_mcangle_other8.50714.7195428
X-RAY DIFFRACTIONr_scbond_it4.70310.1744153
X-RAY DIFFRACTIONr_scbond_other4.68910.154141
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.97215.1836042
X-RAY DIFFRACTIONr_long_range_B_refined13.0719458
X-RAY DIFFRACTIONr_long_range_B_other13.079459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.998→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.386 1778 -
obs--95.39 %
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)
10.33790.37370.06710.44170.08370.018-0.02080.0436-0.00960.05130.0399-0.03370.0122-0.0105-0.01920.340.0882-0.04540.26850.02430.174932.3436119.615166.0681
20.39710.15630.35310.56550.47051.2186-0.0607-0.0469-0.23860.1902-0.07560.08370.0978-0.02560.13620.4791-0.02840.05060.01660.02830.295212.6462128.837147.0324
30.46270.013-1.03490.6953-0.31822.68480.00570.0623-0.01330.0261-0.0266-0.0429-0.16460.07730.02090.3671-0.03130.02240.22240.01970.076540.6258135.0677110.3005
41.50640.3213-0.12961.5991-1.09280.7552-0.15110.03410.18560.34860.13840.0163-0.2188-0.09190.01270.59290.05560.08650.01640.02130.110532.584114.8725141.9627
52.24420.7641.21221.8968-0.06210.82350.117-0.01970.2743-0.1312-0.21050.10890.13930.13050.09360.3160.03840.04250.312-0.06330.138739.8458154.4865124.1586
60.04640.1651-0.03341.40030.06310.8498-0.00090.059-0.0414-0.097-0.14830.00890.04030.05170.14910.37470.04710.00120.2735-0.1140.121515.2686140.64104.9544
70.6709-0.19190.56610.3890.02782.2125-0.090.1440.115-0.05990.00150.08910.1467-0.4440.08860.49040.0359-0.07230.31760.06260.06857.2064160.9883102.7849
80.44230.0848-0.14190.0512-0.01390.0579-0.0315-0.1784-0.07160.0308-0.02350.07640.07830.04560.0550.55480.004-0.09890.10570.01160.33525.9293198.5247135.7891
91.4883-1.1202-1.20970.98940.88011.00260.27120.01830.6786-0.02680.1622-0.771-0.1192-0.0547-0.43330.5462-0.02-0.16010.1491-0.16170.780330.7564178.9228156.2562
100.5835-0.5698-0.0661.4204-0.55950.9905-0.026-0.09680.00970.1199-0.0294-0.1786-0.0832-0.01050.05540.4434-0.0256-0.06520.05790.04180.105822.626156.2617146.7302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-19 - 1
2X-RAY DIFFRACTION2A2 - 252
3X-RAY DIFFRACTION3A253 - 365
4X-RAY DIFFRACTION4A366 - 487
5X-RAY DIFFRACTION5A488 - 590
6X-RAY DIFFRACTION6A591 - 758
7X-RAY DIFFRACTION7A759 - 838
8X-RAY DIFFRACTION8A839 - 864
9X-RAY DIFFRACTION9A865 - 895
10X-RAY DIFFRACTION10A896 - 1066

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