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- PDB-9ux0: Crystal structure of the virulence effector VepA in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9ux0
TitleCrystal structure of the virulence effector VepA in complex with its secretion chaperone VecA
Components
  • Cation transporter
  • CesT family type III secretion system chaperone
KeywordsTOXIN / Vibrio parahaemolyticus / Type 3 secretion system / effector
Function / homologyTir chaperone protein (CesT) family / Tir chaperone protein (CesT) family / protein secretion by the type III secretion system / CesT family type III secretion system chaperone / Cation transporter
Function and homology information
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsIimori, M. / Oki, H. / Akeda, Y. / Ishii, E. / Kodama, T. / Ueda, T. / Nakamura, S. / Matsuda, S. / Kawahara, K. / Iida, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP24KJ1623 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural basis of effector recognition by the T3SS chaperone VecA from Vibrio parahaemolyticus.
Authors: Iimori, M. / Oki, H. / Akeda, Y. / Ishii, E. / Kodama, T. / Ueda, T. / Nakamura, S. / Matsuda, S. / Kawahara, K. / Iida, T.
History
DepositionMay 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cation transporter
B: CesT family type III secretion system chaperone
C: CesT family type III secretion system chaperone


Theoretical massNumber of molelcules
Total (without water)88,2643
Polymers88,2643
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-18 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.848, 152.934, 101.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Cation transporter


Mass: 53156.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP1680 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87P38
#2: Protein CesT family type III secretion system chaperone


Mass: 17553.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: VP1682 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87P37
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100mM sodium cacodylate (pH 6.5), 20% (v/v) PEG 400, 200mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.49→48.26 Å / Num. obs: 29792 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 53.09 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.062 / Rrim(I) all: 0.16 / Χ2: 2.03 / Net I/σ(I): 15 / Num. measured all: 195356
Reflection shellResolution: 2.49→2.59 Å / % possible obs: 99.1 % / Redundancy: 7.3 % / Rmerge(I) obs: 1.108 / Num. measured all: 24194 / Num. unique obs: 3334 / CC1/2: 0.608 / Rpim(I) all: 0.439 / Rrim(I) all: 1.193 / Χ2: 1.04 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→48.26 Å / SU ML: 0.3878 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2764 2907 9.82 %
Rwork0.2406 26705 -
obs0.2441 29612 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.51 Å2
Refinement stepCycle: LAST / Resolution: 2.49→48.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5218 0 0 0 5218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295309
X-RAY DIFFRACTIONf_angle_d0.67657174
X-RAY DIFFRACTIONf_chiral_restr0.038801
X-RAY DIFFRACTIONf_plane_restr0.0061945
X-RAY DIFFRACTIONf_dihedral_angle_d18.18812020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.530.37991450.34751253X-RAY DIFFRACTION98.66
2.53-2.570.36421230.32221278X-RAY DIFFRACTION99.79
2.57-2.620.37031420.32351283X-RAY DIFFRACTION99.1
2.62-2.670.38231270.3251274X-RAY DIFFRACTION99.01
2.67-2.730.38791470.31451245X-RAY DIFFRACTION99.22
2.73-2.790.32371390.30381268X-RAY DIFFRACTION99.36
2.79-2.850.33151480.30481280X-RAY DIFFRACTION98.82
2.85-2.920.361460.3111247X-RAY DIFFRACTION98.86
2.92-30.35221470.29221257X-RAY DIFFRACTION98.73
3-3.090.35641480.30171268X-RAY DIFFRACTION99.09
3.09-3.190.32641290.28621277X-RAY DIFFRACTION98.39
3.19-3.30.34141250.28161272X-RAY DIFFRACTION98.31
3.3-3.430.32311350.26431272X-RAY DIFFRACTION97.98
3.43-3.590.29671340.25041226X-RAY DIFFRACTION95.98
3.59-3.780.30071230.24211274X-RAY DIFFRACTION95.55
3.78-4.020.29211200.22331251X-RAY DIFFRACTION96.35
4.02-4.330.23941410.19511252X-RAY DIFFRACTION95.94
4.33-4.760.20931350.20041280X-RAY DIFFRACTION96.92
4.76-5.450.23691390.19681289X-RAY DIFFRACTION98.41
5.45-6.860.23221540.22361310X-RAY DIFFRACTION99.12
6.87-48.260.22341600.20491349X-RAY DIFFRACTION97.17

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