+Open data
-Basic information
Entry | Database: PDB / ID: 2wct | ||||||
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Title | human SARS coronavirus unique domain (triclinic form) | ||||||
Components | NON-STRUCTURAL PROTEIN 3 | ||||||
Keywords | RNA BINDING PROTEIN / RNA-BINDING PROTEIN / RNA-BINDING / ZINC-FINGER / THIOL PROTEASE / HYDROLASE | ||||||
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 / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / 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 | SARS CORONAVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Tan, J. / Vonrhein, C. / Smart, O.S. / Bricogne, G. / Bollati, M. / Hansen, G. / Mesters, J.R. / Hilgenfeld, R. | ||||||
Citation | Journal: Plos Pathog. / Year: 2009 Title: The Sars-Unique Domain (Sud) of Sars Coronavirus Contains Two Macrodomains that Bind G-Quadruplexes. Authors: Tan, J. / Vonrhein, C. / Smart, O.S. / Bricogne, G. / Bollati, M. / Kusov, Y. / Hansen, G. / Mesters, J.R. / Schmidt, C.L. / Hilgenfeld, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wct.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wct.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wct.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wct_validation.pdf.gz | 457.3 KB | Display | wwPDB validaton report |
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Full document | 2wct_full_validation.pdf.gz | 475.9 KB | Display | |
Data in XML | 2wct_validation.xml.gz | 34.4 KB | Display | |
Data in CIF | 2wct_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/2wct ftp://data.pdbj.org/pub/pdb/validation_reports/wc/2wct | HTTPS FTP |
-Related structure data
Related structure data | 2w2gC 2jzeS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29230.818 Da / Num. of mol.: 4 / Fragment: RESIDUES 1207-1470 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS CORONAVIRUS / Strain: SARS-COV / Plasmid: PQE30-XA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 References: UniProt: P0C6U8, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: 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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 25% PEG MME 5000, 0.1 M MES PH6.5, 0.2 M AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04123 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 27, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04123 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→33.33 Å / Num. obs: 34003 / % possible obs: 93.1 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 80.515 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.8→2.96 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2 / % possible all: 76.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JZE Resolution: 2.79→33.33 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 76.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→33.33 Å
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LS refinement shell | Resolution: 2.79→2.88 Å / Total num. of bins used: 17
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