[English] 日本語
Yorodumi
- PDB-4dvz: Crystal structure of the Helicobacter pylori CagA oncoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dvz
TitleCrystal structure of the Helicobacter pylori CagA oncoprotein
ComponentsCytotoxicity-associated immunodominant antigen
KeywordsONCOPROTEIN
Function / homology
Function and homology information


toxin transmembrane transporter activity / molecular adaptor activity
Similarity search - Function
CagA exotoxin domain III / Type IV secretion system CagA exotoxin / CagA exotoxin, phosphopeptide substrate mimic region / CagA, N-terminal / CagA exotoxin phosphopeptide substrate mimic region / CagA protein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Cytotoxicity-associated immunodominant antigen
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.19 Å
AuthorsHayashi, T. / Senda, M. / Morohashi, H. / Higashi, H. / Horio, M. / Kashiba, Y. / Nagase, L. / Sasaya, D. / Shimizu, T. / Venugopalan, N. ...Hayashi, T. / Senda, M. / Morohashi, H. / Higashi, H. / Horio, M. / Kashiba, Y. / Nagase, L. / Sasaya, D. / Shimizu, T. / Venugopalan, N. / Kumeta, H. / Noda, N. / Inagaki, F. / Senda, T. / Hatakeyama, M.
CitationJournal: Cell Host Microbe / Year: 2012
Title: Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA
Authors: Hayashi, T. / Senda, M. / Morohashi, H. / Higashi, H. / Horio, M. / Kashiba, Y. / Nagase, L. / Sasaya, D. / Shimizu, T. / Venugopalan, N. / Kumeta, H. / Noda, N.N. / Inagaki, F. / Senda, T. / Hatakeyama, M.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)63,6251
Polymers63,6251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.671, 95.671, 167.924
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein Cytotoxicity-associated immunodominant antigen / CagA / CAG pathogenicity island protein 26


Mass: 63625.383 Da / Num. of mol.: 1 / Fragment: UNP residues 261-829
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: cagA / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55980

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7% EtOH, 50mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98057, 0.98086
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2011
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980571
20.980861
ReflectionResolution: 3.19→74.3 Å / Num. all: 15242 / Num. obs: 15242 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 97.02 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 33.39
Reflection shellResolution: 3.19→3.37 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 6 / Num. unique all: 2263 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.19→74.3 Å / Cor.coef. Fo:Fc: 0.9219 / Cor.coef. Fo:Fc free: 0.8671 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 1.611 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.553 / SU Rfree Blow DPI: 0.426 / SU Rfree Cruickshank DPI: 0.435 / Stereochemistry target values: BUSTER
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 1016 6.67 %RANDOM
Rwork0.2215 ---
all0.2253 15242 --
obs0.2253 15242 99.28 %-
Displacement parametersBiso max: 186.4 Å2 / Biso mean: 103.74 Å2 / Biso min: 56 Å2
Baniso -1Baniso -2Baniso -3
1-11.2947 Å20 Å20 Å2
2--11.2947 Å20 Å2
3----22.5895 Å2
Refine analyzeLuzzati coordinate error obs: 0.799 Å
Refinement stepCycle: LAST / Resolution: 3.19→74.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 0 0 3635
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1385SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes133HARMONIC2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it3671HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion468SEMIHARMONIC5
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_contact4061SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3671HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4902HARMONIC21.21
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion24.69
LS refinement shellResolution: 3.19→3.41 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3041 199 7.35 %
Rwork0.2478 2508 -
all0.2518 2707 -
obs--99.28 %

+
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://pdbjlvh1.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