+Open data
-Basic information
Entry | Database: PDB / ID: 2xyr | ||||||
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Title | Crystal structure of the nsp16 nsp10 SARS coronavirus complex | ||||||
Components |
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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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xyr.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xyr.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xyr_validation.pdf.gz | 684.3 KB | Display | wwPDB validaton report |
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Full document | 2xyr_full_validation.pdf.gz | 689.2 KB | Display | |
Data in XML | 2xyr_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 2xyr_validation.cif.gz | 25.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/2xyr ftp://data.pdbj.org/pub/pdb/validation_reports/xy/2xyr | HTTPS FTP |
-Related structure data
Related structure data | 2xyqC 2xyvC 2fygS 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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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32869.695 Da / Num. of mol.: 1 / Fragment: RESIDUES 6776-7067 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 |
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#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, 148 molecules
#3: Chemical | ChemComp-NA / | ||||||||
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#4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-SFG / | #6: Chemical | ChemComp-MG / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 69.81 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 0.1M CHES, 1.52M MGCL2, pH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 21, 2009 / Details: MIRRORS |
Radiation | Monochromator: HORIZONTALLY DIFFRACTING SI (111) MONOCHROMATOR AND PT COATED MIRRORS IN A KIRKPATRICK BAEZ (KB) GEOMETRY Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.58 Å / Num. obs: 28921 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FYG Resolution: 2.5→19.93 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.023 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 50.122 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.93 Å
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Refine LS restraints |
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