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Open data
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Basic information
Entry | Database: PDB / ID: 2xyr | ||||||
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Title | Crystal structure of the nsp16 nsp10 SARS coronavirus complex | ||||||
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![]() | TRANSFERASE/VIRAL PROTEIN / TRANSFERASE-VIRAL PROTEIN COMPLEX / ROSSMANN FOLD | ||||||
Function / homology | ![]() 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 / 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 / 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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Decroly, E. / Debarnot, C. / Ferron, F. / Bouvet, M. / Coutard, B. / Imbert, I. / Gluais, L. / Papageorgiou, N. / Ortiz-Lombardia, M. / Lescar, J. / Canard, B. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.6 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 684.3 KB | Display | ![]() |
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Full document | ![]() | 689.2 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xyqC ![]() 2xyvC ![]() 2fygS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() 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.) ![]() ![]() ![]() |
-Non-polymers , 6 types, 148 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SFG.gif)
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![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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