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- PDB-3tj6: human vinculin head domain (Vh1, residues 1-258) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3tj6
Titlehuman vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding site of the surface cell antigen 4 (sca4-VBS-C; residues 812-835) from Rickettsia rickettsii
Components
  • Antigenic heat-stable 120 kDa protein
  • Vinculin
Keywordsprotein binding/toxin / cytoskeleton / epidemic typhus / sca4 / spotted fever / ALPHA-HELIX BUNDLE DOMAIN / PROTEIN-PROTEIN INTERACTIONS / CELL ADHESION / CYTOSOL / FOCAL ADHESION / protein binding-toxin complex
Function / homology
Function and homology information


regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / fascia adherens / dystroglycan binding ...regulation of protein localization to adherens junction / outer dense plaque of desmosome / inner dense plaque of desmosome / podosome ring / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / fascia adherens / dystroglycan binding / alpha-catenin binding / cell-cell contact zone / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / adherens junction assembly / protein localization to cell surface / lamellipodium assembly / regulation of focal adhesion assembly / maintenance of blood-brain barrier / brush border / Smooth Muscle Contraction / negative regulation of cell migration / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / morphogenesis of an epithelium / cell projection / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / beta-catenin binding / sarcolemma / platelet aggregation / specific granule lumen / 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 / Signaling by ALK fusions and activated point mutants / Platelet degranulation / extracellular vesicle / actin binding / secretory granule lumen / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / 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
Rickettsia surface antigen, 120kDa / 120 KDa Rickettsia surface antigen / 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 ...Rickettsia surface antigen, 120kDa / 120 KDa Rickettsia surface antigen / 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
Antigenic heat-stable 120 kDa protein / Vinculin
Similarity search - Component
Biological speciesHomo sapiens (human)
Rickettsia rickettsii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsPark, H. / Lee, J.H. / Gouin, E. / Cossart, P. / Izard, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The rickettsia surface cell antigen 4 applies mimicry to bind to and activate vinculin.
Authors: Park, H. / Lee, J.H. / Gouin, E. / Cossart, P. / Izard, T.
History
DepositionAug 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 1.2May 1, 2013Group: Other
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vinculin
B: Antigenic heat-stable 120 kDa protein


Theoretical massNumber of molelcules
Total (without water)31,3682
Polymers31,3682
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-24 kcal/mol
Surface area15040 Å2
MethodPISA
2
A: Vinculin
B: Antigenic heat-stable 120 kDa protein

A: Vinculin
B: Antigenic heat-stable 120 kDa protein

A: Vinculin
B: Antigenic heat-stable 120 kDa protein


Theoretical massNumber of molelcules
Total (without water)94,1046
Polymers94,1046
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11800 Å2
ΔGint-91 kcal/mol
Surface area40540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.373, 141.373, 141.373
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Vinculin / Metavinculin


Mass: 28751.188 Da / Num. of mol.: 1
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/peptide Antigenic heat-stable 120 kDa protein / 120 kDa antigen / Protein PS 120 / PS120


Mass: 2616.940 Da / Num. of mol.: 1 / Fragment: unp residues 812-834
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia rickettsii (bacteria) / Strain: Iowa / Gene: RrIowa_0797 / Production host: Escherichia coli (E. coli) / References: UniProt: B0BXR4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.8 Å3/Da / Density % sol: 67.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2% (v/v) tacsimate (pH 5), 100 mM sodium citrate tribasic dihydrate (pH 5.6), 16% (w/v) polyethylene glycol (3,350), 20 mM Tris-HCl (pH 9), 150 mM NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97867 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 10, 2010
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97867 Å / Relative weight: 1
ReflectionResolution: 2.76→99.97 Å / Num. all: 12290 / Num. obs: 12290 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.8 % / Biso Wilson estimate: 72.81 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 36.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.76-2.91150.496.10.491100
2.91-3.081100
3.08-3.31100
3.3-3.561100
3.56-3.91100
3.9-4.361100
4.36-5.031100
5.03-6.161100
6.16-8.721100
8.72-99.96199.8

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
MOLREPphasing
BUSTER2.9.2refinement
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1rkc

1rkc


Resolution: 2.76→44.71 Å / Cor.coef. Fo:Fc: 0.9461 / Cor.coef. Fo:Fc free: 0.9227 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2353 989 8.07 %RANDOM
Rwork0.193 ---
obs0.1963 12251 --
all-12290 --
Displacement parametersBiso mean: 79.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.389 Å
Refinement stepCycle: LAST / Resolution: 2.76→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 0 141 2291
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012175HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.12946HARMONIC2
X-RAY DIFFRACTIONt_omega_torsion2.091058SINUSOIDAL2
X-RAY DIFFRACTIONt_other_torsion3.4366HARMONIC2
LS refinement shellResolution: 2.76→3.02 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2824 243 8.46 %
Rwork0.251 2630 -
all0.2536 2873 -
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)
13.0590.1508-0.82541.0234-0.14651.65290.05080.57970.0834-0.06920.05270.21610.0291-0.3881-0.1035-0.28270.0017-0.0145-0.19840.0948-0.3378-29.75-3.6017-22.183
20.3688.00196.62963.22790.46464.5645-0.00760.18760.0101-0.444-0.11420.0554-0.5203-0.5420.1219-0.09420.0587-0.1120.24370.0238-0.2343-50.5951-3.0693-28.296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|253 }A1 - 253
2X-RAY DIFFRACTION2{ B|812 - B|834 }B812 - 834

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