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Yorodumi- EMDB-11692: Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11692 | |||||||||||||||||||||
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Title | Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP | |||||||||||||||||||||
Map data | Masked EM density map, sharpened by a B-factor of 20 Angstrom^2, used for model building | |||||||||||||||||||||
Sample |
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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 / snRNP Assembly / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / : / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / copper ion binding / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / lipid binding / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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: 2.5 Å | |||||||||||||||||||||
Authors | Naydenova K / Muir KW / Wu LF / Zhang Z / Coscia F / Peet M / Castro-Hartman P / Qian P / Sader K / Dent K ...Naydenova K / Muir KW / Wu LF / Zhang Z / Coscia F / Peet M / Castro-Hartman P / Qian P / Sader K / Dent K / Kimanius D / Sutherland JD / Lowe J / Barford D / Russo CJ | |||||||||||||||||||||
Funding support | United Kingdom, 6 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP. Authors: Katerina Naydenova / Kyle W Muir / Long-Fei Wu / Ziguo Zhang / Francesca Coscia / Mathew J Peet / Pablo Castro-Hartmann / Pu Qian / Kasim Sader / Kyle Dent / Dari Kimanius / John D ...Authors: Katerina Naydenova / Kyle W Muir / Long-Fei Wu / Ziguo Zhang / Francesca Coscia / Mathew J Peet / Pablo Castro-Hartmann / Pu Qian / Kasim Sader / Kyle Dent / Dari Kimanius / John D Sutherland / Jan Löwe / David Barford / Christopher J Russo / Abstract: The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information ...The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11692.map.gz | 14.1 MB | EMDB map data format | |
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Header (meta data) | emd-11692-v30.xml emd-11692.xml | 26 KB 26 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11692_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_11692.png | 123.9 KB | ||
Masks | emd_11692_msk_1.map | 125 MB | Mask map | |
Others | emd_11692_additional.map.gz emd_11692_half_map_1.map.gz emd_11692_half_map_2.map.gz | 98.4 MB 98.4 MB 98.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11692 | HTTPS FTP |
-Related structure data
Related structure data | 7aapMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10517 (Title: Movies of Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-dependent RNA polymerase in complex with template:primer dsRNA and favipiravir-RTP Data size: 46.9 TB Data #1: Unaligned multi-frame micrographs of SARS-CoV-2 RNA-dependent RNA polymerase in compex with template:primer dsRNA and favipiravir-RTP [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11692.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Masked EM density map, sharpened by a B-factor of 20 Angstrom^2, used for model building | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11692_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unsharpened EM density map
File | emd_11692_additional.map | ||||||||||||
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Annotation | Unsharpened EM density map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM density half map 1
File | emd_11692_half_map_1.map | ||||||||||||
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Annotation | EM density half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: EM density half map 2
File | emd_11692_half_map_2.map | ||||||||||||
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Annotation | EM density half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase in complex ...
+Supramolecule #1: Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase in complex ...
+Supramolecule #2: Nsp7-Nsp8-Nsp12 SARS-CoV2 RNA-directed RNA polymerase
+Supramolecule #3: RNA
+Macromolecule #1: Non-structural protein 12
+Macromolecule #2: Non-structural protein 8
+Macromolecule #3: Non-structural protein 7
+Macromolecule #4: RNA (5'-R(P*UP*UP*AP*AP*GP*UP*UP*AP*U)-3')
+Macromolecule #5: RNA (5'-R(P*UP*UP*CP*AP*UP*AP*AP*CP*UP*UP*AP*A)-3')
+Macromolecule #6: ZINC ION
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: PYROPHOSPHATE 2-
+Macromolecule #9: [[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonyl-5-fluoranyl-2-oxid...
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 24.72 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |