+Open data
-Basic information
Entry | Database: PDB / ID: 3cm8 | ||||||
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Title | A RNA polymerase subunit structure from virus | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/Transferase / Protein-peptide Complex / Nucleotide-binding / Nucleotidyltransferase / RNA replication / RNA-directed RNA polymerase / Transferase / RNA BINDING PROTEIN-Transferase COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / viral transcription / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding ...symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / cap snatching / viral transcription / endonuclease activity / host cell cytoplasm / Hydrolases; Acting on ester bonds / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / host cell nucleus / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.899 Å | ||||||
Authors | He, X. / Zhou, J. / Zeng, Z. / Ma, J. / Zhang, R. / Rao, Z. / Liu, Y. | ||||||
Citation | Journal: Nature / Year: 2008 Title: Crystal structure of the polymerase PAC-PB1N complex from an avian influenza H5N1 virus Authors: He, X. / Zhou, J. / Bartlam, M. / Zhang, R. / Ma, J. / Lou, Z. / Li, X. / Li, J. / Joachimiak, A. / Zeng, Z. / Ge, R. / Rao, Z. / Liu, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cm8.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cm8.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 3cm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cm/3cm8 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/3cm8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 53870.789 Da / Num. of mol.: 1 / Fragment: residues in database 256-716 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Environment/Hong Kong/437-6/99 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EA60 |
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#2: Protein/peptide | Mass: 3194.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Hong Kong/156/1997 H5N1 genotype Gs/Gd / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WLS3, RNA-directed RNA polymerase |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 4.38 Å3/Da / Density % sol: 71.94 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1M sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.899→50 Å / Num. all: 23042 / Num. obs: 22964 / % possible obs: 99.7 % / Observed criterion σ(F): 4.6 / Observed criterion σ(I): 4.6 / Biso Wilson estimate: 75.44 Å2 | ||||||||||||||||||
Reflection shell | Highest resolution: 2.899 Å / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.899→45.184 Å / FOM work R set: 0.787 / σ(F): 1.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.261 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.23 Å2 / Biso mean: 84.28 Å2 / Biso min: 166.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.899→45.184 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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