+Open data
-Basic information
Entry | Database: PDB / ID: 2w2g | ||||||
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Title | Human SARS coronavirus unique domain | ||||||
Components | NON-STRUCTURAL PROTEIN 3 | ||||||
Keywords | RNA BINDING PROTEIN / THIOL PROTEASE / RNA REPLICATION / VIRAL REPLICASE / RNA-BINDING / ZINC-FINGER / RIBOSOMAL FRAMESHIFTING / HYDROLASE / RNA-BINDING PROTEIN | ||||||
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 genome replication ...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 genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 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 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease 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 / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | SARS CORONAVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Tan, J. / Vonrhein, C. / Smart, O.S. / Bricogne, G. / Bollati, M. / Kusov, Y. / Hansen, G. / Mesters, J.R. / Schmidt, C.L. / 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 | 2w2g.cif.gz | 114.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w2g.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w2g_validation.pdf.gz | 448 KB | Display | wwPDB validaton report |
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Full document | 2w2g_full_validation.pdf.gz | 453.9 KB | Display | |
Data in XML | 2w2g_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 2w2g_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/2w2g ftp://data.pdbj.org/pub/pdb/validation_reports/w2/2w2g | HTTPS FTP |
-Related structure data
Related structure data | 2wctC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.82507, 0.26201, -0.50061), Vector: |
-Components
#1: Protein | Mass: 29230.818 Da / Num. of mol.: 2 / Fragment: SARS UNIQUE DOMAIN, RESIDUES 1207-1470 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS CORONAVIRUS / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P0C6U8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.52 Å3/Da / Density % sol: 51 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 20% PEGMME 5000,0.2M AMMONIUM SULFATE, 0.1M MES PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.25485 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 2, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.25485 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→28.25 Å / Num. obs: 26598 / % possible obs: 92.1 % / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 48.34 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.22→2.34 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2 / % possible all: 61 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JZE Resolution: 2.22→27.81 Å / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 60.39 Å2
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Refinement step | Cycle: LAST / Resolution: 2.22→27.81 Å
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LS refinement shell | Resolution: 2.22→2.31 Å / Total num. of bins used: 13
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