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- PDB-4irv: Structure of the Helicobacter pylori CagA Oncogene Bound to the H... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4irv | ||||||
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Title | Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor Apoptosis-stimulating Protein of p53-2 | ||||||
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![]() | PROTEIN BINDING / Virulence factor and tumor suppressor | ||||||
Function / homology | ![]() 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 several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cell cycle / NF-kappaB binding ...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 several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cell cycle / NF-kappaB binding / SH3 domain binding / p53 binding / cell junction / molecular adaptor activity / cell cycle / perinuclear region of cytoplasm / signal transduction / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stebbins, C.E. / Nesic, D. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191 KB | Display | ![]() |
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PDB format | ![]() | 160.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 485.3 KB | Display | ![]() |
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Full document | ![]() | 505.4 KB | Display | |
Data in XML | ![]() | 38.8 KB | Display | |
Data in CIF | ![]() | 56 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25480.021 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 6609.313 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.29 % |
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Crystal grow | Method: 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 |
-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→90.75 Å / Num. obs: 80050 |
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Processing
Software | Name: REFMAC / Version: 5.7.0029 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34 Å2
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Refinement step | Cycle: LAST / Resolution: 2.04→90.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.045→2.098 Å / Total num. of bins used: 20
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