[English] 日本語
Yorodumi
- PDB-9ux0: Crystal structure of the virulence effector VepA in complex with ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more