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Yorodumi- PDB-4n0o: Complex structure of Arterivirus nonstructural protein 10 (helica... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n0o | ||||||
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Title | Complex structure of Arterivirus nonstructural protein 10 (helicase) with DNA | ||||||
Components |
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Keywords | HYDROLASE/DNA / arterivirus / helicase / zbd / nsp10 / complex / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 ...serine-type exopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / host cell membrane / RNA nuclease activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Equine arteritis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Deng, Z. / Chen, Z. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase. Authors: Deng, Z. / Lehmann, K.C. / Li, X. / Feng, C. / Wang, G. / Zhang, Q. / Qi, X. / Yu, L. / Zhang, X. / Feng, W. / Wu, W. / Gong, P. / Tao, Y. / Posthuma, C.C. / Snijder, E.J. / Gorbalenya, A.E. / Chen, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n0o.cif.gz | 334.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n0o.ent.gz | 266.3 KB | Display | PDB format |
PDBx/mmJSON format | 4n0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/4n0o ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n0o | HTTPS FTP |
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-Related structure data
Related structure data | 4n0nSC 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 45655.383 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equine arteritis virus / Strain: equine arteritis virusEquine viral arteritis / Gene: 1a-1b, nsp10, rep / Plasmid: pet-28a / Production host: Escherichia coli (E. coli) / Strain (production host): plasmid References: UniProt: P19811, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Serine ...References: UniProt: P19811, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases, RNA-directed RNA polymerase, DNA helicase, RNA helicase #2: DNA chain | Mass: 2084.392 Da / Num. of mol.: 4 / Source method: obtained synthetically #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2M NH4SO4, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 130 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 4, 2012 | |||||||||||||||
Radiation | Monochromator: unknown / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.65→50 Å / Num. all: 69690 / Num. obs: 66954 / % possible obs: 96.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 | |||||||||||||||
Reflection shell | Resolution: 2.65→2.7 Å / % possible all: 95.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4N0N Resolution: 2.65→50 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.89 / SU B: 7.358 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.16 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 48.364 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→50 Å
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Refine LS restraints |
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