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Yorodumi- EMDB-26645: SARS-CoV-2 replication-transcription complex bound to GTP, in a p... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26645 | |||||||||
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Title | SARS-CoV-2 replication-transcription complex bound to GTP, in a pre-catalytic state | |||||||||
Map data | SARS-CoV-2 replication-transcription complex bound to GTP, in a pre-catalytic state | |||||||||
Sample |
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Keywords | RNA-directed 5'-3' RNA polymerase activity / positive stranded viral RNA replication / REPLICATION | |||||||||
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 / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.68 Å | |||||||||
Authors | Malone BF / Perry JK / Appleby TC / Feng JY / Campbell EA / Darst SA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2023 Title: Structural basis for substrate selection by the SARS-CoV-2 replicase. Authors: Brandon F Malone / Jason K Perry / Paul Dominic B Olinares / Hery W Lee / James Chen / Todd C Appleby / Joy Y Feng / John P Bilello / Honkit Ng / Johanna Sotiris / Mark Ebrahim / Eugene Y D ...Authors: Brandon F Malone / Jason K Perry / Paul Dominic B Olinares / Hery W Lee / James Chen / Todd C Appleby / Joy Y Feng / John P Bilello / Honkit Ng / Johanna Sotiris / Mark Ebrahim / Eugene Y D Chua / Joshua H Mendez / Ed T Eng / Robert Landick / Matthias Götte / Brian T Chait / Elizabeth A Campbell / Seth A Darst / Abstract: The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC). Accordingly, the RTC is a target for ...The SARS-CoV-2 RNA-dependent RNA polymerase coordinates viral RNA synthesis as part of an assembly known as the replication-transcription complex (RTC). Accordingly, the RTC is a target for clinically approved antiviral nucleoside analogues, including remdesivir. Faithful synthesis of viral RNAs by the RTC requires recognition of the correct nucleotide triphosphate (NTP) for incorporation into the nascent RNA. To be effective inhibitors, antiviral nucleoside analogues must compete with the natural NTPs for incorporation. How the SARS-CoV-2 RTC discriminates between the natural NTPs, and how antiviral nucleoside analogues compete, has not been discerned in detail. Here, we use cryogenic-electron microscopy to visualize the RTC bound to each of the natural NTPs in states poised for incorporation. Furthermore, we investigate the RTC with the active metabolite of remdesivir, remdesivir triphosphate (RDV-TP), highlighting the structural basis for the selective incorporation of RDV-TP over its natural counterpart adenosine triphosphate. Our results explain the suite of interactions required for NTP recognition, informing the rational design of antivirals. Our analysis also yields insights into nucleotide recognition by the nsp12 NiRAN (nidovirus RdRp-associated nucleotidyltransferase), an enigmatic catalytic domain essential for viral propagation. The NiRAN selectively binds guanosine triphosphate, strengthening proposals for the role of this domain in the formation of the 5' RNA cap. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26645.map.gz | 109.1 MB | EMDB map data format | |
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Header (meta data) | emd-26645-v30.xml emd-26645.xml | 23 KB 23 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26645_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_26645.png | 37.2 KB | ||
Filedesc metadata | emd-26645.cif.gz | 7 KB | ||
Others | emd_26645_additional_1.map.gz emd_26645_half_map_1.map.gz emd_26645_half_map_2.map.gz | 2.9 MB 200.7 MB 200.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26645 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26645 | HTTPS FTP |
-Validation report
Summary document | emd_26645_validation.pdf.gz | 698.5 KB | Display | EMDB validaton report |
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Full document | emd_26645_full_validation.pdf.gz | 698.1 KB | Display | |
Data in XML | emd_26645_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | emd_26645_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26645 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26645 | HTTPS FTP |
-Related structure data
Related structure data | 7uobMC 7uo4C 7uo7C 7uo9C 7uoeC 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_26645.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | SARS-CoV-2 replication-transcription complex bound to GTP, in a pre-catalytic state | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Local resolution filtered map
File | emd_26645_additional_1.map | ||||||||||||
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Annotation | Local resolution filtered map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 replication-transcription complex bound to GTP, in a...
File | emd_26645_half_map_1.map | ||||||||||||
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Annotation | SARS-CoV-2 replication-transcription complex bound to GTP, in a pre-catalytic state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: SARS-CoV-2 replication-transcription complex bound to GTP, in a...
File | emd_26645_half_map_2.map | ||||||||||||
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Annotation | SARS-CoV-2 replication-transcription complex bound to GTP, in a pre-catalytic state | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : SARS-CoV-2 replication-transcription complex + GTP
+Supramolecule #1: SARS-CoV-2 replication-transcription complex + GTP
+Macromolecule #1: RNA-directed RNA polymerase
+Macromolecule #2: Non-structural protein 8
+Macromolecule #3: Non-structural protein 7
+Macromolecule #4: Product RNA (35-MER)
+Macromolecule #5: Template RNA (55-MER)
+Macromolecule #6: ZINC ION
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #9: 3'-DEOXYURIDINE-5'-MONOPHOSPHATE
+Macromolecule #10: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.44 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: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |