+
Open data
-
Basic information
Entry | Database: PDB / ID: 8osx | ||||||
---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 nsp10-16 methyltransferase in complex with ATP | ||||||
![]() |
| ||||||
![]() | VIRAL PROTEIN / methyltransferase / complex / inhibitor | ||||||
Function / homology | ![]() protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / 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 suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / SARS-CoV-2 modulates host translation machinery / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / 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 endoplasmic reticulum membrane / 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 / copper ion binding / 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 / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kremling, V. / Sprenger, J. / Oberthuer, D. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Crystal structures of Tubercidin and Adenosine bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16 Authors: Kremling, V. / Sprenger, J. / Oberthuer, D. / Yefanov, O. / Galchenkova, M. / Middendorf, P. / Falke, S. / Garcia, Y. / Ehrt, C. / Kiene, A. / Klopprogge, B. / Chapman, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 136.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 82.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bzvC ![]() 8c5mC ![]() 8ot0C ![]() 8otoC ![]() 8otrC ![]() 8ov1C ![]() 8ov2C ![]() 8ov3C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 34150.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() |
---|---|
#2: Protein | Mass: 14859.983 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() |
-Non-polymers , 7 types, 275 molecules ![](data/chem/img/ATP.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/SAM.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ATP / | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-MES / | #6: Chemical | ChemComp-SAM / | #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.25 Å3/Da / Density % sol: 71.05 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 900 mM sodium fluoride, 100 mM 2-(N-morpholino)ethanesulfonic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03321 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→42.14 Å / Num. obs: 73616 / % possible obs: 99.55 % / Redundancy: 8.2 % / Biso Wilson estimate: 37.7 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1951 / Rrim(I) all: 0.2083 / Net I/σ(I): 6.85 |
Reflection shell | Resolution: 1.83→1.895 Å / Redundancy: 8.4 % / Rmerge(I) obs: 3.118 / Mean I/σ(I) obs: 0.27 / Num. unique obs: 7157 / CC1/2: 0.18 / CC star: 0.552 / Rrim(I) all: 3.324 / % possible all: 97.77 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→42.14 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|