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Yorodumi- PDB-3ebn: A Special Dimerization of SARS-CoV Main Protease C-Terminal Domai... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ebn | ||||||
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Title | A Special Dimerization of SARS-CoV Main Protease C-Terminal Domain Due to Domain-swapping | ||||||
Components | Replicase polyprotein 1ab | ||||||
Keywords | HYDROLASE / SARS / coronavirus / main protease / dimerization / N-finger / C-terminal domain | ||||||
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 / viral transcription / SARS-CoV-1 modulates host translation machinery ...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 / viral transcription / SARS-CoV-1 modulates host translation machinery / 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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / 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 / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Zhong, N. / Zhang, S. / Xue, F. / Kang, X. / Lou, Z. / Xia, B. | ||||||
Citation | Journal: PROTEIN SCI. / Year: 2009 Title: C-terminal domain of SARS-CoV main protease can form a 3D domain-swapped dimer Authors: Zhong, N. / Zhang, S. / Xue, F. / Kang, X. / Zou, P. / Chen, J. / Liang, C. / Rao, Z. / Jin, C. / Lou, Z. / Xia, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ebn.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ebn.ent.gz | 68.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ebn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ebn_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 3ebn_full_validation.pdf.gz | 452.6 KB | Display | |
Data in XML | 3ebn_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 3ebn_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/3ebn ftp://data.pdbj.org/pub/pdb/validation_reports/eb/3ebn | HTTPS FTP |
-Related structure data
Related structure data | 2k7xC 1uk2S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13010.697 Da / Num. of mol.: 4 / Fragment: UNP residues 3429-3546 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS coronavirus / Gene: rep, 1a-1b / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta References: UniProt: P0C6X7, 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: 1.99 Å3/Da / Density % sol: 38.28 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG3350, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2007 / Details: osmic mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 15252 / Num. obs: 14727 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.19 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UK2 Resolution: 2.4→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.4→50 Å
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Refine LS restraints |
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