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Yorodumi- EMDB-28666: Cryo-EM structure of SARS-CoV-2 Main protease C145S in complex wi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28666 | |||||||||
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Title | Cryo-EM structure of SARS-CoV-2 Main protease C145S in complex with N-terminal peptide | |||||||||
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Keywords | covid19 / mpro / main protease / cryo-Em / 3cl / sars-cov-2 / VIRAL PROTEIN | |||||||||
Function / homology | Function and homology information 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 / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 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 / 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 / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / 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 / host cell endoplasmic reticulum membrane / 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 / 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 / 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 | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Noske GD / Song Y / Fernandes RS / Oliva G / Godoy AS | |||||||||
Funding support | Brazil, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition. Authors: Gabriela Dias Noske / Yun Song / Rafaela Sachetto Fernandes / Rod Chalk / Haitem Elmassoudi / Lizbé Koekemoer / C David Owen / Tarick J El-Baba / Carol V Robinson / / Glaucius Oliva / Andre Schutzer Godoy / Abstract: The main protease from SARS-CoV-2 (M) is responsible for cleavage of the viral polyprotein. M self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use ...The main protease from SARS-CoV-2 (M) is responsible for cleavage of the viral polyprotein. M self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S M to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of M N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the M dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_28666.map.gz | 40.4 MB | EMDB map data format | |
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Header (meta data) | emd-28666-v30.xml emd-28666.xml | 18 KB 18 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_28666_fsc.xml | 7.5 KB | Display | FSC data file |
Images | emd_28666.png | 50.8 KB | ||
Masks | emd_28666_msk_1.map | 44 MB | Mask map | |
Filedesc metadata | emd-28666.cif.gz | 5.8 KB | ||
Others | emd_28666_additional_1.map.gz emd_28666_half_map_1.map.gz emd_28666_half_map_2.map.gz | 21.6 MB 40.8 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28666 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28666 | HTTPS FTP |
-Validation report
Summary document | emd_28666_validation.pdf.gz | 979.4 KB | Display | EMDB validaton report |
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Full document | emd_28666_full_validation.pdf.gz | 979 KB | Display | |
Data in XML | emd_28666_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_28666_validation.cif.gz | 19.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28666 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28666 | HTTPS FTP |
-Related structure data
Related structure data | 8ey2MC 8eyjC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_28666.map.gz / Format: CCP4 / Size: 44 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.653 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_28666_msk_1.map | ||||||||||||
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-Additional map: #1
File | emd_28666_additional_1.map | ||||||||||||
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-Half map: #1
File | emd_28666_half_map_1.map | ||||||||||||
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-Half map: #2
File | emd_28666_half_map_2.map | ||||||||||||
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-Sample components
-Entire : Cryo-EM structure of SARS-CoV-2 Main protease C145S mutant
Entire | Name: Cryo-EM structure of SARS-CoV-2 Main protease C145S mutant |
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Components |
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-Supramolecule #1: Cryo-EM structure of SARS-CoV-2 Main protease C145S mutant
Supramolecule | Name: Cryo-EM structure of SARS-CoV-2 Main protease C145S mutant type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 68 kDa/nm |
-Macromolecule #1: 3C-like proteinase
Macromolecule | Name: 3C-like proteinase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: SARS coronavirus main proteinase |
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Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Molecular weight | Theoretical: 34.567371 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GAMSAVLQSG FRKMAFPSGK VEGCMVQVTC GTTTLNGLWL DDVVYCPRHV ICTSEDMLNP NYEDLLIRKS NHNFLVQAGN VQLRVIGHS MQNCVLKLKV DTANPKTPKY KFVRIQPGQT FSVLACYNGS PSGVYQCAMR PNFTIKGSFL NGSSGSVGFN I DYDCVSFC ...String: GAMSAVLQSG FRKMAFPSGK VEGCMVQVTC GTTTLNGLWL DDVVYCPRHV ICTSEDMLNP NYEDLLIRKS NHNFLVQAGN VQLRVIGHS MQNCVLKLKV DTANPKTPKY KFVRIQPGQT FSVLACYNGS PSGVYQCAMR PNFTIKGSFL NGSSGSVGFN I DYDCVSFC YMHHMELPTG VHAGTDLEGN FYGPFVDRQT AQAAGTDTTI TVNVLAWLYA AVINGDRWFL NRFTTTLNDF NL VAMKYNY EPLTQDHVDI LGPLSAQTGI AVLDMCASLK ELLQNGMNGR TILGSALLED EFTPFDVVRQ CSGVTFQ UniProtKB: Replicase polyprotein 1ab |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.25 mg/mL |
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Buffer | pH: 7.8 Details: 20 mM Tris pH 7.8, 150 mM NaCl, 1 mM EDTA, 1 mM DTT |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 13770 / Average electron dose: 43.38557582 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |