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Yorodumi- PDB-6r0t: Getah virus macro domain in complex with ADPr in open conformation -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r0t | ||||||
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Title | Getah virus macro domain in complex with ADPr in open conformation | ||||||
Components | Non-structural polyprotein | ||||||
Keywords | VIRAL PROTEIN / Macro domain / Getah virus | ||||||
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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping ...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 / symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / 7-methylguanosine mRNA capping / cysteine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / Transferases; Transferring one-carbon groups; Methyltransferases / 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 / 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 | Getah virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å | ||||||
Authors | Ferreira Ramos, A.S. / Sulzenbacher, G. / Coutard, B. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Snapshots of ADP-ribose bound to Getah virus macro domain reveal an intriguing choreography. Authors: Ferreira-Ramos, A.S. / Sulzenbacher, G. / Canard, B. / Coutard, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r0t.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r0t.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 6r0t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r0t_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6r0t_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6r0t_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 6r0t_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/6r0t ftp://data.pdbj.org/pub/pdb/validation_reports/r0/6r0t | HTTPS FTP |
-Related structure data
Related structure data | 6qzuSC 6r0fC 6r0gC 6r0pC 6r0rC 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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Unit cell |
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-Components
#1: Protein | Mass: 18120.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: synthetic gene / Source: (gene. exp.) Getah virus / Gene: nsP1234 / Plasmid: pDest14 Details (production host): from ThermoFischer, Gateway cloning Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: A0A143SL92, UniProt: Q5Y389*PLUS #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 2.28 Å3/Da / Density % sol: 45.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.9 Details: Imidazole-Malate pH 5.9, 34% PEG 4K, 3 mM ADPr, 30mM Aspartic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jan 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40.68 Å / Num. obs: 28867 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.051 / Rrim(I) all: 0.087 / Rsym value: 0.071 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1.107 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1757 / CC1/2: 0.627 / Rpim(I) all: 0.792 / Rrim(I) all: 1.369 / Rsym value: 1.107 / % possible all: 99.8 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6QZU Resolution: 1.85→33.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.561 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 43.258 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→33.98 Å
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