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Yorodumi- PDB-5c8s: Crystal structure of the SARS coronavirus nsp14-nsp10 complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c8s | |||||||||||||||
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Title | Crystal structure of the SARS coronavirus nsp14-nsp10 complex with functional ligands SAH and GpppA | |||||||||||||||
Components |
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Keywords | TRANSFERASE / nsp14 / nsp10 / exoribonuclease / methyltransferase | |||||||||||||||
Function / homology | Function and homology information Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral transcription ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral transcription / Transferases; Transferring one-carbon groups; Methyltransferases / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | |||||||||||||||
Biological species | Human SARS coronavirus | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.326 Å | |||||||||||||||
Authors | Ma, Y.Y. / Wu, L.J. / Zhang, R.G. / Rao, Z.H. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structural basis and functional analysis of the SARS coronavirus nsp14-nsp10 complex Authors: Ma, Y.Y. / Wu, L.J. / Shaw, N. / Gao, Y. / Wang, J. / Sun, Y.N. / Lou, Z.Y. / Yan, L.M. / Zhang, R.G. / Rao, Z.H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c8s.cif.gz | 267.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c8s.ent.gz | 221 KB | Display | PDB format |
PDBx/mmJSON format | 5c8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c8s_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 5c8s_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 5c8s_validation.xml.gz | 58 KB | Display | |
Data in CIF | 5c8s_validation.cif.gz | 77.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/5c8s ftp://data.pdbj.org/pub/pdb/validation_reports/c8/5c8s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15268.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human SARS coronavirus / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6X7 #2: Protein | Mass: 59967.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human SARS coronavirus / Production host: Escherichia coli (E. coli) References: UniProt: P0C6X7, Transferases; Transferring one-carbon groups; Methyltransferases, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
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-Non-polymers , 4 types, 16 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | #6: Chemical | |
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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: 5.58 Å3/Da / Density % sol: 78.97 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% (v/v) tacsimate pH 7.0, 0.1 M HEPES pH 7.0, and 2% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→50 Å / Num. obs: 50763 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 111.12 Å2 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Χ2: 0.445 / Net I/av σ(I): 16.5 / Net I/σ(I): 4.3 / Num. measured all: 339184 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 3.326→42.558 Å / FOM work R set: 0.7604 / SU ML: 0.94 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 86 Å2 / ksol: 0.32 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 213.27 Å2 / Biso mean: 124.96 Å2 / Biso min: 64.32 Å2
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Refinement step | Cycle: final / Resolution: 3.326→42.558 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: 18
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