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- PDB-4irv: Structure of the Helicobacter pylori CagA Oncogene Bound to the H... -

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Basic information

Entry
Database: PDB / ID: 4irv
TitleStructure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2
Components
  • Apoptosis-stimulating of p53 protein 2
  • Cytotoxicity-associated immunodominant antigen
KeywordsPROTEIN BINDING / Virulence factor and tumor suppressor
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / toxin transmembrane transporter activity / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of cell cycle / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of execution phase of apoptosis ...symbiont-mediated perturbation of host cell cycle progression / toxin transmembrane transporter activity / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of cell cycle / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of execution phase of apoptosis / NF-kappaB binding / SH3 domain binding / p53 binding / cell junction / molecular adaptor activity / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Tetracycline Repressor; domain 2 - #130 / : / Type IV secretion system CagA exotoxin / CagA exotoxin, phosphopeptide substrate mimic region / CagA, N-terminal / : / : / CagA exotoxin phosphopeptide substrate mimic region / CagA protein / Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain ...Tetracycline Repressor; domain 2 - #130 / : / Type IV secretion system CagA exotoxin / CagA exotoxin, phosphopeptide substrate mimic region / CagA, N-terminal / : / : / CagA exotoxin phosphopeptide substrate mimic region / CagA protein / Apoptosis-stimulating of p53 protein 2-like, N-terminal RA domain / Tetracycline Repressor; domain 2 / SH3 domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cytotoxicity-associated immunodominant antigen / Apoptosis-stimulating of p53 protein 2
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsStebbins, C.E. / Nesic, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of the Helicobacter pylori CagA oncoprotein bound to the human tumor suppressor ASPP2.
Authors: Nesic, D. / Buti, L. / Lu, X. / Stebbins, C.E.
History
DepositionJan 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxicity-associated immunodominant antigen
B: Cytotoxicity-associated immunodominant antigen
C: Cytotoxicity-associated immunodominant antigen
D: Cytotoxicity-associated immunodominant antigen
E: Apoptosis-stimulating of p53 protein 2
F: Apoptosis-stimulating of p53 protein 2
G: Apoptosis-stimulating of p53 protein 2
H: Apoptosis-stimulating of p53 protein 2


Theoretical massNumber of molelcules
Total (without water)128,3578
Polymers128,3578
Non-polymers00
Water9,242513
1
A: Cytotoxicity-associated immunodominant antigen
E: Apoptosis-stimulating of p53 protein 2


Theoretical massNumber of molelcules
Total (without water)32,0892
Polymers32,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-17 kcal/mol
Surface area10500 Å2
MethodPISA
2
B: Cytotoxicity-associated immunodominant antigen
F: Apoptosis-stimulating of p53 protein 2


Theoretical massNumber of molelcules
Total (without water)32,0892
Polymers32,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-17 kcal/mol
Surface area10350 Å2
MethodPISA
3
C: Cytotoxicity-associated immunodominant antigen
G: Apoptosis-stimulating of p53 protein 2


Theoretical massNumber of molelcules
Total (without water)32,0892
Polymers32,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-17 kcal/mol
Surface area10600 Å2
MethodPISA
4
D: Cytotoxicity-associated immunodominant antigen
H: Apoptosis-stimulating of p53 protein 2


Theoretical massNumber of molelcules
Total (without water)32,0892
Polymers32,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-17 kcal/mol
Surface area10550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.641, 120.239, 100.659
Angle α, β, γ (deg.)90.00, 115.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

21B-342-

HOH

31B-363-

HOH

41C-380-

HOH

51D-303-

HOH

61D-357-

HOH

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Components

#1: Protein
Cytotoxicity-associated immunodominant antigen / 120 kDa protein / CAG pathogenicity island protein 26


Mass: 25480.021 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: cagA, cag26, cai, HP_0547 / Production host: Escherichia coli (E. coli) / References: UniProt: P55980
#2: Protein
Apoptosis-stimulating of p53 protein 2 / Bcl2-binding protein / Bbp / Renal carcinoma antigen NY-REN-51 / Tumor suppressor p53-binding ...Bcl2-binding protein / Bbp / Renal carcinoma antigen NY-REN-51 / Tumor suppressor p53-binding protein 2 / 53BP2 / p53-binding protein 2 / p53BP2


Mass: 6609.313 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPP2, BBP, TP53BP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13625
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) ...Details: Crystals were grown by vapor diffusion at 25 degrees C using hanging drops formed from mixing a 2ul of the protein complex with 2ul of an equilibration buffer (21% polyethylene glycol (PEG) molecular weight 4 kDa, 200 mM Li2 SO4 , and 100 mM Tris pH 8.5) and 0.6ul of the Silver Bullets additive 43 (Hampton Research HR2-996-43). Significantly higher quality crystals were obtained from selenomethionine-substituted protein complexes and they were used for the final refinement, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97869 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.04→90.75 Å / Num. obs: 80050

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Processing

SoftwareName: REFMAC / Version: 5.7.0029 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.04→90.75 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.95 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 3915 5 %RANDOM
Rwork0.18927 ---
obs0.19148 73785 96.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å20 Å20.24 Å2
2---0.99 Å20 Å2
3---2 Å2
Refinement stepCycle: LAST / Resolution: 2.04→90.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7017 0 0 513 7530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.027145
X-RAY DIFFRACTIONr_bond_other_d0.0020.026818
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9479603
X-RAY DIFFRACTIONr_angle_other_deg0.904315722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83425.718390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.826151301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.421536
X-RAY DIFFRACTIONr_chiral_restr0.1170.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.045→2.098 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 247 -
Rwork0.228 4839 -
obs--85.9 %

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