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- PDB-7cwc: Ambient-Temperature Serial Femtosecond X-ray Crystal structure of... -
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Basic information
Entry | Database: PDB / ID: 7cwc | |||||||||
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Title | Ambient-Temperature Serial Femtosecond X-ray Crystal structure of SARS-CoV-2 Main Protease at 2.1 A Resolution (P212121) | |||||||||
![]() | 3C-like proteinase | |||||||||
![]() | VIRAL PROTEIN / COVID19 / SARS-CoV-2 / Drug Target / Serial Femtosecond X-ray Crystallography / SFX / XFEL / Virus Protein | |||||||||
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 | ![]() ![]() ![]() ![]() | |||||||||
![]() | DeMirci, H. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing. Authors: Durdagi, S. / Dag, C. / Dogan, B. / Yigin, M. / Avsar, T. / Buyukdag, C. / Erol, I. / Ertem, F.B. / Calis, S. / Yildirim, G. / Orhan, M.D. / Guven, O. / Aksoydan, B. / Destan, E. / Sahin, K. ...Authors: Durdagi, S. / Dag, C. / Dogan, B. / Yigin, M. / Avsar, T. / Buyukdag, C. / Erol, I. / Ertem, F.B. / Calis, S. / Yildirim, G. / Orhan, M.D. / Guven, O. / Aksoydan, B. / Destan, E. / Sahin, K. / Besler, S.O. / Oktay, L. / Shafiei, A. / Tolu, I. / Ayan, E. / Yuksel, B. / Peksen, A.B. / Gocenler, O. / Yucel, A.D. / Can, O. / Ozabrahamyan, S. / Olkan, A. / Erdemoglu, E. / Aksit, F. / Tanisali, G. / Yefanov, O.M. / Barty, A. / Tolstikova, A. / Ketawala, G.K. / Botha, S. / Dao, E.H. / Hayes, B. / Liang, M. / Seaberg, M.H. / Hunter, M.S. / Batyuk, A. / Mariani, V. / Su, Z. / Poitevin, F. / Yoon, C.H. / Kupitz, C. / Sierra, R.G. / Snell, E.H. / DeMirci, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.3 KB | Display | ![]() |
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PDB format | ![]() | 203.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 439.1 KB | Display | ![]() |
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Full document | ![]() | 446.2 KB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cwbC ![]() 6wqfS ![]() 7wcb 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
#1: Protein | Mass: 34239.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: rep, 1a-1b / Production host: ![]() ![]() References: UniProt: P0DTD1, SARS coronavirus main proteinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.8 % |
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Crystal grow | Temperature: 294 K / Method: batch mode Details: 0.2 M Sodium acetate trihydrate, 0.1 M Tris 8.5, 30 % w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 294 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Aug 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.25 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→42 Å / Num. obs: 45380 / % possible obs: 100 % / Redundancy: 3105 % / CC1/2: 0.997 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.1→2.2 Å / Num. unique obs: 4468 / CC1/2: 0.6288725 |
-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6wqf Resolution: 2.1→41.977 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.57 Å2 / Biso mean: 64.9627 Å2 / Biso min: 27.58 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→41.977 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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