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Yorodumi- PDB-3iec: Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mim... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iec | ||||||
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Title | Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates | ||||||
Components |
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Keywords | SIGNALING PROTEIN/TOXIN / Protein-protein complex / kinase / virulence factor / Alternative promoter usage / ATP-binding / Cell membrane / Developmental protein / Differentiation / Magnesium / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / SIGNALING PROTEIN-TOXIN COMPLEX | ||||||
Function / homology | Function and homology information establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / regulation of microtubule binding / mitochondrion localization / toxin transmembrane transporter activity / autophagy of mitochondrion / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of cytoskeleton organization / regulation of axonogenesis ...establishment or maintenance of cell polarity regulating cell shape / microtubule bundle / regulation of microtubule binding / mitochondrion localization / toxin transmembrane transporter activity / autophagy of mitochondrion / tau-protein kinase / establishment or maintenance of epithelial cell apical/basal polarity / regulation of cytoskeleton organization / regulation of axonogenesis / establishment of cell polarity / tau-protein kinase activity / axon development / protein kinase activator activity / activation of protein kinase activity / lateral plasma membrane / regulation of microtubule cytoskeleton organization / actin filament / peptidyl-threonine phosphorylation / neuron migration / tau protein binding / positive regulation of neuron projection development / microtubule cytoskeleton organization / Wnt signaling pathway / peptidyl-serine phosphorylation / protein autophosphorylation / molecular adaptor activity / non-specific serine/threonine protein kinase / intracellular signal transduction / cadherin binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / lipid binding / magnesium ion binding / mitochondrion / RNA binding / nucleoplasm / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Stebbins, C.E. / Nesic, D. / Miller, M. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Helicobacter pylori CagA inhibits PAR1-MARK family kinases by mimicking host substrates. Authors: Nesic, D. / Miller, M.C. / Quinkert, Z.T. / Stein, M. / Chait, B.T. / Stebbins, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iec.cif.gz | 289.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iec.ent.gz | 231.6 KB | Display | PDB format |
PDBx/mmJSON format | 3iec.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/3iec ftp://data.pdbj.org/pub/pdb/validation_reports/ie/3iec | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 36919.777 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 49-363 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CagA, EMK1, MARK2 / Production host: Escherichia coli (E. coli) References: UniProt: Q7KZI7, non-specific serine/threonine protein kinase #2: Protein | Mass: 13423.082 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 885-1005 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: strain 26695 / Gene: cagA, cai / Production host: Escherichia coli (E. coli) / References: UniProt: P55980 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% ...Details: Initial crystals were grown by vapor diffusion using hanging drops formed from mixing a 2:1 volume ratio of the protein complex with an equilibration buffer consisting of 22.5-25% polyethylene glycol (PEG) molecular weight 3350 Da, 300 mM Li2SO4, and 100 mM Bis-Tris pH 5.8-6.2, at 23 C. Higher quality crystals were obtained by micro-seeding and addition of 5% PEG 400 as an additive. For cryoprotection crystals where transferred directly into a buffer with a 25% PEG 3350 Da, 5-10% PEG 400 Da, 300mM Li2SO4, 100mM Bis-Tris pH 5.8-6.2, 7.5% glycerol, and flash-cooled immediately afterward to -160 C. , VAPOR DIFFUSION, HANGING DROP, temperature 296K PH range: 5.8 - 6.2 |
-Data collection
Diffraction | Mean temperature: 103 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2008 Details: Beamline X29 features high-flux radiation derived from a 54-pole harmonic emission undulator, a vertically focusing mirror and a horizontally focusing monochromator. A Cryomech AL300 is ...Details: Beamline X29 features high-flux radiation derived from a 54-pole harmonic emission undulator, a vertically focusing mirror and a horizontally focusing monochromator. A Cryomech AL300 is utilized to produce extremely stable cooling on a Si(111) crystal. The beamline is capable of delivering an energy range of 7-15 kev | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. obs: 97843 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.089 / Χ2: 1.04 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40.96 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.82 / SU B: 12.78 / SU ML: 0.145 / SU R Cruickshank DPI: 0.224 / SU Rfree: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.223 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 76.53 Å2 / Biso mean: 26.151 Å2 / Biso min: 5.02 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→40.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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