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- PDB-7b3d: Structure of elongating SARS-CoV-2 RNA-dependent RNA polymerase w... -

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Basic information

Entry
Database: PDB / ID: 7b3d
TitleStructure of elongating SARS-CoV-2 RNA-dependent RNA polymerase with AMP at position -4 (structure 3)
Components
  • RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3')
  • RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3')
  • SARS-CoV-2 RNA-dependent RNA polymerase nsp12
  • SARS-CoV-2 nsp7
  • SARS-CoV-2 nsp8
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Polymerase / Transcription / Replication / RNA / Remdesivir / Inhibition / Nucleotide Analogue
Function / homology
Function and homology information


Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation ...Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / exoribonuclease activity / RNA phosphodiester bond hydrolysis, exonucleolytic / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / G-quadruplex RNA binding / 3'-5'-exoribonuclease activity / suppression by virus of host ISG15-protein conjugation / suppression by virus of host toll-like receptor signaling pathway / host cell endoplasmic reticulum-Golgi intermediate compartment / protein K48-linked deubiquitination / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / viral genome replication / suppression by virus of host TRAF activity / helicase activity / viral transcription / Transferases; Transferring one-carbon groups; Methyltransferases / ubiquitinyl hydrolase 1 / DNA helicase / methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / thiol-dependent deubiquitinase / DNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / methylation / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / endonuclease activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / viral RNA genome replication / RNA helicase activity / suppression by virus of host type I interferon-mediated signaling pathway / viral protein processing / Hydrolases; Acting on ester bonds / transcription, DNA-templated / host cell cytoplasm / protein dimerization 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 / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 14, betacoronavirus / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus proofreading exoribonuclease / Coronavirus 2'-O-methyltransferase / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Sarbecovirus Nsp3c-N domain profile. / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein 2, SARS-CoV-like / Polyprotein cleavage domain PL2pro superfamily, coronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Betacoronavirus replicase NSP1 / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Coronavirus (CoV) Nsp1 globular domain profile. / Non-structural protein 6, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Lipocalin signature. / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus papain-like peptidase / Coronavirus replicase NSP6 / Coronavirus endopeptidase C30 / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP8, coronavirus-like / Coronavirus replicase NSP4, N-terminal / Non-structural protein NSP8 superfamily, coronavirus / Peptidase C30, coronavirus / Coronavirus main protease (M-pro) domain profile. / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Coronavirus replicase NSP4, N-terminal / RNA synthesis protein NSP10, coronavirus / Coronavirus replicase NSP3, C-terminal / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus
Similarity search - Domain/homology
RNA (> 10) / RNA / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKokic, G. / Hillen, H.S. / Tegunov, D. / Dienemann, C. / Seitz, F. / Schmitzova, J. / Farnung, L. / Siewert, A. / Hoebartner, C. / Cramer, P.
Funding support Germany, 7items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2848 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
German Research Foundation (DFG)SPP1784 Germany
European Research Council (ERC)682586 Germany
European Research Council (ERC)693023 Germany
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of SARS-CoV-2 polymerase stalling by remdesivir.
Authors: Goran Kokic / Hauke S Hillen / Dimitry Tegunov / Christian Dienemann / Florian Seitz / Jana Schmitzova / Lucas Farnung / Aaron Siewert / Claudia Höbartner / Patrick Cramer /
Abstract: Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of ...Remdesivir is the only FDA-approved drug for the treatment of COVID-19 patients. The active form of remdesivir acts as a nucleoside analog and inhibits the RNA-dependent RNA polymerase (RdRp) of coronaviruses including SARS-CoV-2. Remdesivir is incorporated by the RdRp into the growing RNA product and allows for addition of three more nucleotides before RNA synthesis stalls. Here we use synthetic RNA chemistry, biochemistry and cryo-electron microscopy to establish the molecular mechanism of remdesivir-induced RdRp stalling. We show that addition of the fourth nucleotide following remdesivir incorporation into the RNA product is impaired by a barrier to further RNA translocation. This translocation barrier causes retention of the RNA 3'-nucleotide in the substrate-binding site of the RdRp and interferes with entry of the next nucleoside triphosphate, thereby stalling RdRp. In the structure of the remdesivir-stalled state, the 3'-nucleotide of the RNA product is matched and located with the template base in the active center, and this may impair proofreading by the viral 3'-exonuclease. These mechanistic insights should facilitate the quest for improved antivirals that target coronavirus replication.
History
DepositionNov 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 3, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

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Assembly

Deposited unit
A: SARS-CoV-2 RNA-dependent RNA polymerase nsp12
B: SARS-CoV-2 nsp8
C: SARS-CoV-2 nsp7
P: RNA (5'-R(P*CP*UP*AP*CP*GP*CP*AP*GP*UP*G)-3')
T: RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,8277
Polymers161,6965
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area11000 Å2
ΔGint-103 kcal/mol
Surface area41370 Å2
MethodPISA

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein SARS-CoV-2 RNA-dependent RNA polymerase nsp12 / pp1ab / ORF1ab polyprotein


Mass: 107053.227 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: Trichoplusia ni (cabbage looper)
References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein SARS-CoV-2 nsp8 / pp1ab / ORF1ab polyprotein


Mass: 22175.309 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: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases
#3: Protein SARS-CoV-2 nsp7 / pp1ab / ORF1ab polyprotein


Mass: 9521.062 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: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL
References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA ...References: UniProt: P0DTD1, ubiquitinyl hydrolase 1, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, SARS coronavirus main proteinase, RNA-directed RNA polymerase, DNA helicase, RNA helicase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds, Transferases; Transferring one-carbon groups; Methyltransferases

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RNA chain , 2 types, 2 molecules PT

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


Mass: 4807.914 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#5: RNA chain RNA (5'-R(P*UP*GP*CP*AP*CP*UP*GP*CP*GP*UP*AP*G)-3')


Mass: 18138.658 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Non-polymers , 1 types, 2 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
1SARS-CoV-2 RNA-dependent RNA polymerase complex (nsp12, nsp7, nsp8) with elongation scaffold containing AMP at position -4.COMPLEX#1-#50MULTIPLE SOURCES
2SARS-CoV-2 RNA-dependent RNA polymerase nsp12COMPLEX#11RECOMBINANT
3SARS-CoV-2 nsp7 and 8COMPLEX#2-#31RECOMBINANT
4DNA and RNACOMPLEX#4-#51RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Severe acute respiratory syndrome coronavirus 22697049
23Severe acute respiratory syndrome coronavirus 22697049
34Severe acute respiratory syndrome coronavirus 22697049
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Trichoplusia ni (cabbage looper)7111
23Escherichia coli BL21(DE3) (bacteria)469008
34synthetic construct (others)32630
Buffer solutionpH: 7.4
Buffer component
IDConc.FormulaBuffer-ID
120 mMHepes1
2100 mMNaClSodium chloride1
31 mMMgCl21
41 mMTCEP1
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: 30 deg tilt.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 105000 X / Calibrated defocus min: 0.4 nm / Calibrated defocus max: 1.7 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Warp1.0.7particle selection
2SerialEM3.8image acquisition
4Warp1.0.7CTF correction
7Coot0.9model fitting
9PHENIX1.18model refinement
12cryoSPARCclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1767915
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 819273 / Details: M was used / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 6YYT

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