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- PDB-7dfh: Structure of COVID-19 RNA-dependent RNA polymerase bound to ribavirin -

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Basic information

Entry
Database: PDB / ID: 7dfh
TitleStructure of COVID-19 RNA-dependent RNA polymerase bound to ribavirin
Components
  • (Non-structural protein ...Viral nonstructural protein) x 2
  • RNA (5'-R(P*CP*CP*CP*CP*CP*AP*CP*AP*UP*AP*GP*C)-3')
  • RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*G*(LIG))-3')
  • RNA-directed RNA polymeras
KeywordsVIRAL PROTEIN/RNA / COVID-19 / RNA polymerase / ribavirin binding / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / 5'-3' RNA helicase activity ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / mRNA cap binding complex / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Lyases; Phosphorus-oxygen lyases / positive regulation of RNA biosynthetic process / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / RNA-templated transcription / viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / suppression by virus of host toll-like receptor signaling pathway / host cell Golgi apparatus / host cell endoplasmic reticulum / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive regulation of viral genome replication / suppression by virus of host TRAF activity / protein autoprocessing / cysteine-type peptidase activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / cysteine-type deubiquitinase activity / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / integral to membrane of host cell / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / DNA-templated transcription / host cell cytoplasm / protein dimerization activity / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus replicase NSP15, N-terminal oligomerization / Non-structural protein NSP15, middle domain superfamily / RNA polymerase, N-terminal, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 15, middle domain, coronavirus / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / Carbamoyl-phosphate synthase subdomain signature 2. / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Lipocalin signature. / : / : / : / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M domain profile. / : / Non-structural protein NSP3, SUD-M domain, betacoronavirus / NSP1, globular domain, betacoronavirus / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein 6, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus replicase NSP2, C-terminal / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP4, C-terminal / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, N-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Coronavirus replicase NSP3, C-terminal / Peptidase C30, coronavirus
Similarity search - Domain/homology
PYROPHOSPHATE 2- / RNA (> 10) / RNA / RIBAVIRIN MONOPHOSPHATE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsLi, Z. / Zhou, Z. / Yu, X.
CitationJournal: 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. ...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
DepositionNov 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: RNA-directed RNA polymeras
B: Non-structural protein 8
C: Non-structural protein 7
G: Non-structural protein 8
P: RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*G*(LIG))-3')
T: RNA (5'-R(P*CP*CP*CP*CP*CP*AP*CP*AP*UP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,56714
Polymers167,6886
Non-polymers8808
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area14830 Å2
ΔGint-142 kcal/mol
Surface area48210 Å2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA-directed RNA polymeras


Mass: 107965.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTD1, RNA-directed RNA polymerase

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Non-structural protein ... , 2 types, 3 molecules BGC

#2: Protein Non-structural protein 8


Mass: 22034.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTD1
#3: Protein Non-structural protein 7


Mass: 9380.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0DTD1

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RNA chain , 2 types, 2 molecules PT

#4: RNA chain RNA (5'-R(P*GP*CP*UP*AP*UP*GP*UP*G*(LIG))-3')


Mass: 2543.545 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#5: RNA chain RNA (5'-R(P*CP*CP*CP*CP*CP*AP*CP*AP*UP*AP*GP*C)-3')


Mass: 3730.304 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Non-polymers , 5 types, 10 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-RVP / RIBAVIRIN MONOPHOSPHATE


Mass: 324.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: COVID-19 RdRp complex bound to favipiravir / Type: COMPLEX / Entity ID: #1-#3, #5 / Source: RECOMBINANT
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 68 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196511 / Symmetry type: POINT

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