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Yorodumi- EMDB-30795: Structure of COVID-19 RNA-dependent RNA polymerase (extended conf... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30795 | |||||||||
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Title | Structure of COVID-19 RNA-dependent RNA polymerase (extended conformation) bound to penciclovir | |||||||||
Map data | ||||||||||
Sample |
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Keywords | COVID-19 / RNA polymerase in extended conformation / penciclovir binding / 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: 2.73 Å | |||||||||
Authors | Li Z / Yu X | |||||||||
Citation | Journal: To Be Published Title: Structural basis for repurpose and design of nucleotide drugs for treating COVID-19 Authors: Yin W / Luan X / Li Z / Xie Y / Zhou Z / Liu J / Gao M / Wang X / Zhou F / Wang Q / Wang Q / Shen D / Zhang Y / Tian G / Aisa H / Wei D / Jiang Y / Xiao G / Jiang H / Zhang L / Yu X / Shen J / Zhang S / Xu H | |||||||||
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_30795.map.gz | 60 MB | EMDB map data format | |
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Header (meta data) | emd-30795-v30.xml emd-30795.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
Images | emd_30795.png | 146.1 KB | ||
Filedesc metadata | emd-30795.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30795 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30795 | HTTPS FTP |
-Validation report
Summary document | emd_30795_validation.pdf.gz | 622.7 KB | Display | EMDB validaton report |
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Full document | emd_30795_full_validation.pdf.gz | 622.3 KB | Display | |
Data in XML | emd_30795_validation.xml.gz | 6 KB | Display | |
Data in CIF | emd_30795_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30795 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30795 | HTTPS FTP |
-Related structure data
Related structure data | 7dokMC 7dfgC 7dfhC 7doiC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30795.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.069 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : COVID-19 RdRp complex (exntended conformation) bound to penciclovir
+Supramolecule #1: COVID-19 RdRp complex (exntended conformation) bound to penciclovir
+Macromolecule #1: RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*GP*AP*GP*AP*UP*UP*AP*AP*GP*UP*UP...
+Macromolecule #2: RNA (5'-R(P*CP*CP*CP*UP*AP*UP*AP*AP*CP*UP*UP*AP*AP*UP*CP*UP*CP*AP...
+Macromolecule #3: RNA-directed RNA polymerase
+Macromolecule #4: Non-structural protein 8
+Macromolecule #5: Non-structural protein 7
+Macromolecule #6: [(2R)-4-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-(hydroxymethyl...
+Macromolecule #7: MAGNESIUM ION
+Macromolecule #8: ZINC ION
+Macromolecule #9: PYROPHOSPHATE 2-
+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: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 68.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139773 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |