+Open data
-Basic information
Entry | Database: PDB / ID: 2xyq | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the nsp16 nsp10 SARS coronavirus complex | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/VIRAL PROTEIN / TRANSFERASE-VIRAL PROTEIN COMPLEX / ROSSMANN FOLD | ||||||
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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / 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 / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / 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 / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding Similarity search - Function | ||||||
Biological species | SARS CORONAVIRUS | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Decroly, E. / Debarnot, C. / Ferron, F. / Bouvet, M. / Coutard, B. / Imbert, I. / Gluais, L. / Papageorgiou, N. / Ortiz-Lombardia, M. / Lescar, J. / Canard, B. | ||||||
Citation | Journal: Plos Pathog. / Year: 2011 Title: Crystal Structure and Functional Analysis of the Sars-Coronavirus RNA CAP 2'-O-Methyltransferase Nsp10/Nsp16 Complex. Authors: Decroly, E. / Debarnot, C. / Ferron, F. / Bouvet, M. / Coutard, B. / Imbert, I. / Gluais, L. / Papageorgiou, N. / Sharff, A. / Bricogne, G. / Ortiz-Lombardia, M. / Lescar, J. / Canard, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xyq.cif.gz | 104.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xyq.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 2xyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xyq ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xyq | HTTPS FTP |
---|
-Related structure data
Related structure data | 2xyrC 2xyvC 2fygS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32695.537 Da / Num. of mol.: 1 / Fragment: RESIDUES 6776-7065 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS CORONAVIRUS / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 References: UniProt: P0C6X7, Transferases; Transferring one-carbon groups; Methyltransferases |
---|---|
#2: Protein | Mass: 13048.936 Da / Num. of mol.: 1 / Fragment: RESIDUES 4240-4361 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SARS CORONAVIRUS / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P0C6X7 |
-Non-polymers , 6 types, 306 molecules
#3: Chemical | #4: Chemical | ChemComp-SAH / | #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 69.81 % / Description: NONE |
---|---|
Crystal grow | pH: 9 / Details: 0.1M CHES, 1.52M MGCL2, pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 15, 2010 / Details: MIRRORS |
Radiation | Monochromator: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.52 Å / Num. obs: 54947 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.7 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FYG Resolution: 2→37.24 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.113 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.161 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→37.24 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|