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Yorodumi- PDB-4o42: Tandem chromodomains of human CHD1 in complex with influenza NS1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o42 | ||||||
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Title | Tandem chromodomains of human CHD1 in complex with influenza NS1 C-terminal tail dimethylated at K229 | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/VIRAL PROTEIN / viral / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC / DNA BINDING PROTEIN-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / methylated histone binding / helicase activity / histone binding ...symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / nucleosome organization / positive regulation by host of viral transcription / ATP-dependent chromatin remodeler activity / nuclear chromosome / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / methylated histone binding / helicase activity / histone binding / Estrogen-dependent gene expression / DNA helicase / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / chromatin remodeling / chromatin binding / host cell nucleus / chromatin / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å | ||||||
Authors | Qin, S. / Xu, C. / Tempel, W. / Arrowsmith, C.H. / Bountra, C. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Structural basis for histone mimicry and hijacking of host proteins by influenza virus protein NS1. Authors: Qin, S. / Liu, Y. / Tempel, W. / Eram, M.S. / Bian, C. / Liu, K. / Senisterra, G. / Crombet, L. / Vedadi, M. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o42.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o42.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o42_validation.pdf.gz | 441.9 KB | Display | wwPDB validaton report |
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Full document | 4o42_full_validation.pdf.gz | 441.9 KB | Display | |
Data in XML | 4o42_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 4o42_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/4o42 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/4o42 | HTTPS FTP |
-Related structure data
Related structure data | 4nw2C 4o45C 4o46C 2b2wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 22942.408 Da / Num. of mol.: 1 / Fragment: UNP residues 268-443 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHD1 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: O14646, DNA helicase | ||||
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#2: Protein/peptide | Mass: 1819.269 Da / Num. of mol.: 1 / Fragment: UNP residues 216-230 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Influenza A virus / References: UniProt: Q38SQ2 | ||||
#3: Chemical | ChemComp-UNX / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.2 % |
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Crystal grow | Temperature: 291 K / pH: 7 Details: 15% PEG3350, 0.1 succinic acid, pH 7, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å | ||||||||||||||||||
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 3, 2012 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.87→46.06 Å / Num. obs: 20229 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.3 | ||||||||||||||||||
Reflection shell | Rmerge(I) obs: 0.012 / Diffraction-ID: 1
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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 Starting model: PDB ENTRY 2B2W Resolution: 1.87→46.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2131 / WRfactor Rwork: 0.1825 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8353 / SU B: 6.096 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1249 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: coot was used for interactive model building. Model geometry was assessed with molprobity.
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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: 130.25 Å2 / Biso mean: 41.1586 Å2 / Biso min: 17.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→46.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.919 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -13.2516 Å / Origin y: -12.1436 Å / Origin z: 14.2216 Å
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