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- PDB-3tj5: human vinculin head domain (Vh1, residues 1-258) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3tj5
Titlehuman vinculin head domain (Vh1, residues 1-258) in complex with the vinculin binding site of the surface cell antigen 4 (sca4-VBS-N; residues 412-434) 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 / podosome ring / outer dense plaque of desmosome / inner dense plaque of desmosome / terminal web / cell-substrate junction / 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 / terminal web / cell-substrate junction / epithelial cell-cell adhesion / zonula adherens / dystroglycan binding / alpha-catenin binding / fascia adherens / cell-cell contact zone / adherens junction assembly / apical junction assembly / costamere / regulation of establishment of endothelial barrier / axon extension / 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 / cell-matrix adhesion / cell projection / morphogenesis of an epithelium / adherens junction / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / sarcolemma / beta-catenin binding / 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 / Signaling by BRAF and RAF1 fusions / cell-cell junction / extracellular vesicle / Signaling by ALK fusions and activated point mutants / 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 / cytoplasm / cytosol
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 str. Iowa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,4693
Polymers31,3772
Non-polymers921
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-28 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.404, 76.343, 114.549
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Vinculin / Metavinculin


Mass: 28565.021 Da / Num. of mol.: 1 / Fragment: unp residues 1-255
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


Mass: 2812.165 Da / Num. of mol.: 1 / Fragment: unp residues 412-434
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia rickettsii str. Iowa (bacteria)
Strain: Iowa / Gene: RrIowa_0797, sca4 / Production host: Escherichia coli (E. coli) / References: UniProt: B0BXR4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.79 Å3/Da / Density % sol: 67.55 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 0.1 M MES monohydrate pH 6.5, 14% PEG 20,000, 20 mM Tris-HCl pH 8, 150 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL11-111
2
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDJul 10, 2010
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTALSINGLE WAVELENGTHMx-ray1
2ASYMMETRIC CUT 4.965 DEGREESx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→114.55 Å / Num. obs: 33356 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 39.37 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 26.3
Reflection shellResolution: 1.99→2.1 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.499 / % possible all: 100

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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: 1.99→23.39 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1681 5.05 %RANDOM
Rwork0.194 ---
obs0.195 33271 --
all-33356 --
Displacement parametersBiso mean: 52.66 Å2
Baniso -1Baniso -2Baniso -3
1--10.8495 Å20 Å20 Å2
2---2.4525 Å20 Å2
3---13.302 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 1.99→23.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2176 0 6 316 2498
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012304HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.993108HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.33
X-RAY DIFFRACTIONt_other_torsion2.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 1.99→2.05 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2601 129 4.74 %
Rwork0.2349 2590 -
all0.2361 2719 -
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)
10.2470.6613-0.70791.3834-2.45393.8457-0.14030.0558-0.0488-0.2660.1263-0.0730.4492-0.17120.014-0.012300.0504-0.1003-0.0088-0.1004-25.0953-6.477918.7588
23.2336-0.9468-0.27891.5875-2.08914.6145-0.00380.17850.30930.024-0.0081-0.229-0.39090.06350.01190.0311-0.052-0.0424-0.03380.0108-0.0302-21.8824-7.214840.4398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|255 }A2 - 255
2X-RAY DIFFRACTION2{ B|408 - B|434 }B408 - 434

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