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Yorodumi- PDB-2j98: Human coronavirus 229E non structural protein 9 cys69ala mutant (Nsp9) -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j98 | ||||||
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Title | Human coronavirus 229E non structural protein 9 cys69ala mutant (Nsp9) | ||||||
Components | (REPLICASE POLYPROTEIN 1AB) x 2 | ||||||
Keywords | RNA BINDING PROTEIN / SSB / HCOV / MEMBRANE / HELICASE / SARS COV / VIRAL REPLICASE / RNA REPLICATION / ATP-BINDING / NUCLEOTIDE-BINDING / RIBOSOMAL FRAMESHIFT / RNA-BINDING PROTEIN | ||||||
Function / homology | Function and homology information host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity ...host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / 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 / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | HUMAN CORONAVIRUS 229E | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ponnusamy, R. / Mesters, J.R. / Moll, R. / Hilgenfeld, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Variable Oligomerization Modes in Coronavirus Non-Structural Protein 9. Authors: Ponnusamy, R. / Moll, R. / Weimar, T. / Mesters, J.R. / Hilgenfeld, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j98.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j98.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 2j98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j98 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j98 | HTTPS FTP |
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-Related structure data
Related structure data | 2j97C 1qz8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9975, -0.0703, -0.000359), Vector: |
-Components
#1: Protein | Mass: 12028.768 Da / Num. of mol.: 1 / Fragment: RESIDUES 3825-3933 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN CORONAVIRUS 229E / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C6U2, UniProt: P0C6X1*PLUS |
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#2: Protein | Mass: 12026.752 Da / Num. of mol.: 1 / Fragment: RESIDUES 3825-3933 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN CORONAVIRUS 229E / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C6U2, UniProt: P0C6X1*PLUS |
#3: Chemical | ChemComp-DTT / |
#4: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.08 % / Description: NONE |
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Crystal grow | pH: 4.5 / Details: 0.1M NA ACETATE PH 4.6 30% PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8075 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 18, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8075 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→30 Å / Num. obs: 17889 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.74→1.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.07 / % possible all: 44.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QZ8 Resolution: 1.8→53.68 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.371 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 1,2 AND 107,108 FROM CHAIN A, RESIDUES 1-4 FROM CHAIN B ARE DISORDERED.CHAIN A RESIDUES 55REMARK OCCUPANCIES SET TO ZERO. VIZIER. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 1,2 AND 107,108 FROM CHAIN A, RESIDUES 1-4 FROM CHAIN B ARE DISORDERED.CHAIN A RESIDUES 55REMARK OCCUPANCIES SET TO ZERO. VIZIER.VIRAL ENZYMES INVOLVED IN REPLICATION.
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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: 34.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→53.68 Å
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