+
Open data
-
Basic information
Entry | Database: PDB / ID: 9fx6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of Cryo2RT SARS-CoV-2 main protease at 100K | |||||||||
![]() | 3C-like proteinase nsp5 | |||||||||
![]() | VIRAL PROTEIN / cryo2RT / synchrotron / room-temperature / protein | |||||||||
Function / homology | ![]() viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase ...viral genome replication / methyltransferase 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 / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / 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 / host cell endoplasmic reticulum membrane / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / lipid binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huang, C.Y. / Aumonier, S. / Mac Sweeney, A. / Olieric, V. / Wang, M. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Cryo2RT: a high-throughput method for room-temperature macromolecular crystallography from cryo-cooled crystals. Authors: Huang, C.Y. / Aumonier, S. / Olieric, V. / Wang, M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 137.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 105.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 454 KB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7h56C ![]() 7h57C ![]() 7h58C ![]() 7h59C ![]() 7h5aC ![]() 7h5bC ![]() 7h5cC ![]() 7h5dC ![]() 7h5eC ![]() 7h5fC ![]() 7h5gC ![]() 7h5hC ![]() 7h5iC ![]() 7h5jC ![]() 7h5kC ![]() 7h5lC ![]() 7h5mC ![]() 7h5nC ![]() 7h5oC ![]() 7h5pC ![]() 7h5qC ![]() 7h5rC ![]() 7h5sC ![]() 7h5tC ![]() 7h5uC ![]() 7h5vC ![]() 7h5wC ![]() 7h5xC ![]() 7h5yC ![]() 7h5zC ![]() 9fx4C ![]() 9fx5C ![]() 9fx7C C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 33825.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P0DTC1, SARS coronavirus main proteinase #2: Chemical | ChemComp-DMS / #3: Chemical | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 300 mM sodium nitrate, 300 mM disodium hydrogen phosphate, 300 mM ammonium sulphate, 100 mM MES/imidazole pH 6.5, 10% (w/v) PEG550 MME and 20% (w/v) PEG 20K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2024 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.227→71.71 Å / Num. obs: 34960 / % possible obs: 99.6 % / Redundancy: 6.58 % / CC1/2: 0.99 / Rrim(I) all: 0.17 / Net I/σ(I): 8.35 |
Reflection shell | Resolution: 2.23→2.36 Å / Redundancy: 6.54 % / Mean I/σ(I) obs: 1.45 / Num. unique obs: 5537 / CC1/2: 0.55 / Rrim(I) all: 1.43 / % possible all: 99.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.01 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.227→29.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.23→2.24 Å / Total num. of bins used: 51
|