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- PDB-6fq4: Structure of Chlamydial virulence factor TarP and vinculin head domain -

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Basic information

Entry
Database: PDB / ID: 6fq4
TitleStructure of Chlamydial virulence factor TarP and vinculin head domain
Components
  • TarP-VBS1
  • Vinculin
KeywordsCELL ADHESION / Translocated Actin Recruitment Protein / vinculin-binding site / virulence factor / Protein complex
Function / homology
Function and homology information


muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens ...muscle tendon junction / Platelet degranulation / Smooth Muscle Contraction / regulation of protein localization to adherens junction / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / vinculin binding / muscle alpha-actinin binding / MAP2K and MAPK activation / 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 / alpha-actinin binding / brush border / skeletal muscle myofibril / stress fiber / regulation of cell migration / cell projection / Neutrophil degranulation / morphogenesis of an epithelium / adherens junction / sarcolemma / neuromuscular junction / Z disc / beta-catenin binding / actin filament binding / cell-cell junction / actin cytoskeleton / scaffold protein binding / mitochondrial inner membrane / cytoskeleton / 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
Domain of unknown function DUF1547 / Domain of Unknown Function (DUF1547) / 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 ...Domain of unknown function DUF1547 / Domain of Unknown Function (DUF1547) / 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
Vinculin / DUF1547 domain-containing protein
Similarity search - Component
Biological speciesGallus gallus (chicken)
Chlamydia caviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsWhitewood, A.J. / Singh, A.K. / Brown, D.G. / Goult, B.T.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N007336/1 United Kingdom
Human Frontier Science Program (HFSP)RGP00001/2016
CitationJournal: FEBS Lett. / Year: 2018
Title: Chlamydial virulence factor TarP mimics talin to disrupt the talin-vinculin complex.
Authors: Whitewood, A.J. / Singh, A.K. / Brown, D.G. / Goult, B.T.
History
DepositionFeb 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Vinculin
B: TarP-VBS1


Theoretical massNumber of molelcules
Total (without water)33,5112
Polymers33,5112
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-18 kcal/mol
Surface area14850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.807, 66.873, 95.832
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Vinculin / / Metavinculin


Mass: 31327.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-259 / Source: (gene. exp.) Gallus gallus (chicken) / Gene: VCL, VINC1 / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12003
#2: Protein/peptide TarP-VBS1


Mass: 2183.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: residues 850-868 / Source: (synth.) Chlamydia caviae (bacteria) / References: UniProt: Q824H6*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.65 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dehydrate pH 5.6, 20% 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2016 / Details: CRL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.89→95.83 Å / Num. obs: 7888 / % possible obs: 99.8 % / Redundancy: 6.1 % / CC1/2: 0.994 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.07 / Rrim(I) all: 0.171 / Net I/σ(I): 8.1
Reflection shellResolution: 2.89→3.05 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1131 / CC1/2: 0.903 / Rpim(I) all: 0.355 / Rrim(I) all: 0.882 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZDL

3zdl


Resolution: 2.89→95.83 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.888 / SU B: 40.822 / SU ML: 0.693 / Cross valid method: THROUGHOUT / ESU R Free: 0.539
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U values refined individually
RfactorNum. reflection% reflectionSelection details
Rfree0.34593 410 5.2 %RANDOM
Rwork0.28607 ---
obs0.28944 7455 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 92.076 Å2
Baniso -1Baniso -2Baniso -3
1--9.58 Å20 Å20 Å2
2--22.3 Å20 Å2
3----12.72 Å2
Refinement stepCycle: 1 / Resolution: 2.89→95.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 0 3 2085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192104
X-RAY DIFFRACTIONr_bond_other_d0.0030.022076
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9852845
X-RAY DIFFRACTIONr_angle_other_deg1.14334824
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.635266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.52325.23884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.86515413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0751513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212262
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02359
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_it3.5069.1131070
X-RAY DIFFRACTIONr_mcbond_other3.4969.1141069
X-RAY DIFFRACTIONr_mcangle_it5.69913.6751334
X-RAY DIFFRACTIONr_mcangle_other5.69813.6741335
X-RAY DIFFRACTIONr_scbond_it3.5449.6711031
X-RAY DIFFRACTIONr_scbond_other3.5359.6711031
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.23414.3191512
X-RAY DIFFRACTIONr_long_range_B_refined10.968936
X-RAY DIFFRACTIONr_long_range_B_other10.9598937
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.891→2.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.622 28 -
Rwork0.471 519 -
obs--100 %

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