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- PDB-4dvy: Crystal structure of the Helicobacter pylori CagA oncoprotein -

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Basic information

Entry
Database: PDB / ID: 4dvy
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
Tetracycline Repressor; domain 2 - #130 / 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 / Tetracycline Repressor; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...Tetracycline Repressor; domain 2 - #130 / 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 / Tetracycline Repressor; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cytotoxicity-associated immunodominant antigen
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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 1.1Aug 22, 2012Group: Structure summary
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Cytotoxicity-associated immunodominant antigen


Theoretical massNumber of molelcules
Total (without water)98,4431
Polymers98,4431
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)97.307, 97.307, 244.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 98442.992 Da / Num. of mol.: 1 / Fragment: UNP residues 1-876 / Mutation: H131M/L274M
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

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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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 8% EtOH, 50mM Tris-HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 18, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.3→90.42 Å / Num. all: 18403 / Num. obs: 18403 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 102.76 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 25.23
Reflection shellResolution: 3.3→3.58 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 4.42 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DVZ

4dvz


Resolution: 3.3→90.42 Å / Cor.coef. Fo:Fc: 0.9458 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.432 / Stereochemistry target values: BUSTER
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1035 5.62 %RANDOM
Rwork0.1905 ---
all0.1936 18403 --
obs0.1936 18403 99.49 %-
Displacement parametersBiso max: 266.86 Å2 / Biso mean: 145.89 Å2 / Biso min: 71.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.9782 Å20 Å20 Å2
2--2.9782 Å20 Å2
3----5.9564 Å2
Refine analyzeLuzzati coordinate error obs: 0.958 Å
Refinement stepCycle: LAST / Resolution: 3.3→90.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5229 0 0 0 5229
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1978SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes190HARMONIC2
X-RAY DIFFRACTIONt_gen_planes728HARMONIC5
X-RAY DIFFRACTIONt_it5297HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion681SEMIHARMONIC5
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_contact6151SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5297HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7091HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion2.35
X-RAY DIFFRACTIONt_other_torsion22.92
LS refinement shellResolution: 3.3→3.5 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.282 157 5.37 %
Rwork0.2241 2769 -
all0.2272 2926 -
obs--99.49 %
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)
11.5144-2.2312-1.76284.34151.96120.21060.2271-0.39730.5442-0.0920.090.4001-0.5442-0.0619-0.3171-0.10160.152-0.1086-0.304-0.1520.2688-3.672960.9234-5.4883
25.5541.54662.91042.66481.63693.87060.1487-0.484-0.22070.1935-0.11350.11490.4214-0.3522-0.0352-0.3040.04880.09610.0996-0.0264-0.304-16.177320.4527-23.7424
31.5397-0.00910.04861.2523-0.96270.7453-0.0954-0.06240.25990.5442-0.0954-0.0884-0.54420.01630.19080.2245-0.1359-0.1504-0.0701-0.0965-0.304-20.789741.9101-47.7488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ P|24 - P|221 }P24 - 221
2X-RAY DIFFRACTION2{ P|303 - P|648 }P303 - 648
3X-RAY DIFFRACTION3{ P|649 - P|824 }P649 - 824

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