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Yorodumi- PDB-6w7h: Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w7h | ||||||
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Title | Co-crystal structures of CHIKV nsP3 macrodomain with pyrimidone fragments | ||||||
Components | Nonstructural polyprotein | ||||||
Keywords | VIRAL PROTEIN / nsP3 / Macrodomain / pyrimidone fragments | ||||||
Function / homology | Function and homology information host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity ...host cell filopodium / ADP-ribose 1''-phosphate phosphatase / mRNA methyltransferase activity / mRNA 5'-triphosphate monophosphatase activity / mRNA 5'-phosphatase / polynucleotide 5'-phosphatase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulation of cytoskeleton organization / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / nucleoside-triphosphate phosphatase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / GTP binding / host cell plasma membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Chikungunya virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å | ||||||
Authors | Zhang, S. / Garzan, A. / Augelli-Szafran, C.E. / Pathak, A.K. / Wu, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Plos One / Year: 2021 Title: Pyrimidone inhibitors targeting Chikungunya Virus nsP3 macrodomain by fragment-based drug design. Authors: Zhang, S. / Garzan, A. / Haese, N. / Bostwick, R. / Martinez-Gzegozewska, Y. / Rasmussen, L. / Streblow, D.N. / Haise, M.T. / Pathak, A.K. / Augelli-Szafran, C.E. / Wu, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w7h.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w7h.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 6w7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w7h ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w7h | HTTPS FTP |
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-Related structure data
Related structure data | 6vuqSC 6w0tC 6w8kC 6w8mC 6w8qC 6w8yC 6w8zC 6w91C 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 18518.877 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4D6GPC4, UniProt: Q8JUX6*PLUS #2: Chemical | ChemComp-TEV / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.52 Å3/Da / Density % sol: 51.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 21-24% PEG 400, 0.1 M sodium citrate pH5.6, 10% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→74.52 Å / Num. obs: 49164 / % possible obs: 100 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.95→2.05 Å / Rmerge(I) obs: 0.547 / Num. unique obs: 3698 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VUQ Resolution: 1.95→56.33 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.974 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.162 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.51 Å2 / Biso mean: 36.98 Å2 / Biso min: 15.55 Å2
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Refinement step | Cycle: final / Resolution: 1.95→56.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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