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- EMDB-13135: SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand bas... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-13135 | ||||||||||||||||||
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Title | SARS-CoV-2 RdRp with Molnupiravir/ NHC in the template strand base-paired with A | ||||||||||||||||||
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![]() | SARS-CoV-2 / RNA-dependent RNA polymerase / Molnupiravir (NHC) / VIRAL PROTEIN | ||||||||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||||||||
![]() | Kabinger F / Stiller C | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Authors: Florian Kabinger / Carina Stiller / Jana Schmitzová / Christian Dienemann / Goran Kokic / Hauke S Hillen / Claudia Höbartner / Patrick Cramer / ![]() Abstract: Molnupiravir is an orally available antiviral drug candidate currently in phase III trials for the treatment of patients with COVID-19. Molnupiravir increases the frequency of viral RNA mutations and ...Molnupiravir is an orally available antiviral drug candidate currently in phase III trials for the treatment of patients with COVID-19. Molnupiravir increases the frequency of viral RNA mutations and impairs SARS-CoV-2 replication in animal models and in humans. Here, we establish the molecular mechanisms underlying molnupiravir-induced RNA mutagenesis by the viral RNA-dependent RNA polymerase (RdRp). Biochemical assays show that the RdRp uses the active form of molnupiravir, β-D-N-hydroxycytidine (NHC) triphosphate, as a substrate instead of cytidine triphosphate or uridine triphosphate. When the RdRp uses the resulting RNA as a template, NHC directs incorporation of either G or A, leading to mutated RNA products. Structural analysis of RdRp-RNA complexes that contain mutagenesis products shows that NHC can form stable base pairs with either G or A in the RdRp active center, explaining how the polymerase escapes proofreading and synthesizes mutated RNA. This two-step mutagenesis mechanism probably applies to various viral polymerases and can explain the broad-spectrum antiviral activity of molnupiravir. #1: ![]() Title: Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis Authors: Kabinger F / Stiller C / Schmitzova J / Dienemann C / Hillen HS / Hobartner C / Cramer P | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 48.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.8 KB 19.8 KB | Display Display | ![]() |
Images | ![]() | 106.4 KB | ||
Masks | ![]() | 52.7 MB | ![]() | |
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 40.9 MB 40.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ozuMC ![]() 7ozvC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_13135_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_13135_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : RdRp
Entire | Name: RdRp |
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Components |
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-Supramolecule #1: RdRp
Supramolecule | Name: RdRp / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Molecular weight | Theoretical: 183.81 kDa/nm |
-Macromolecule #1: Replicase polyprotein 1ab
Macromolecule | Name: Replicase polyprotein 1ab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 106.780977 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: SADAQSFLNR VCGVSAARLT PCGTGTSTDV VYRAFDIYND KVAGFAKFLK TNCCRFQEKD EDDNLIDSYF VVKRHTFSNY QHEETIYNL LKDCPAVAKH DFFKFRIDGD MVPHISRQRL TKYTMADLVY ALRHFDEGNC DTLKEILVTY NCCDDDYFNK K DWYDFVEN ...String: SADAQSFLNR VCGVSAARLT PCGTGTSTDV VYRAFDIYND KVAGFAKFLK TNCCRFQEKD EDDNLIDSYF VVKRHTFSNY QHEETIYNL LKDCPAVAKH DFFKFRIDGD MVPHISRQRL TKYTMADLVY ALRHFDEGNC DTLKEILVTY NCCDDDYFNK K DWYDFVEN PDILRVYANL GERVRQALLK TVQFCDAMRN AGIVGVLTLD NQDLNGNWYD FGDFIQTTPG SGVPVVDSYY SL LMPILTL TRALTAESHV DTDLTKPYIK WDLLKYDFTE ERLKLFDRYF KYWDQTYHPN CVNCLDDRCI LHCANFNVLF STV FPPTSF GPLVRKIFVD GVPFVVSTGY HFRELGVVHN QDVNLHSSRL SFKELLVYAA DPAMHAASGN LLLDKRTTCF SVAA LTNNV AFQTVKPGNF NKDFYDFAVS KGFFKEGSSV ELKHFFFAQD GNAAISDYDY YRYNLPTMCD IRQLLFVVEV VDKYF DCYD GGCINANQVI VNNLDKSAGF PFNKWGKARL YYDSMSYEDQ DALFAYTKRN VIPTITQMNL KYAISAKNRA RTVAGV SIC STMTNRQFHQ KLLKSIAATR GATVVIGTSK FYGGWHNMLK TVYSDVENPH LMGWDYPKCD RAMPNMLRIM ASLVLAR KH TTCCSLSHRF YRLANECAQV LSEMVMCGGS LYVKPGGTSS GDATTAYANS VFNICQAVTA NVNALLSTDG NKIADKYV R NLQHRLYECL YRNRDVDTDF VNEFYAYLRK HFSMMILSDD AVVCFNSTYA SQGLVASIKN FKSVLYYQNN VFMSEAKCW TETDLTKGPH EFCSQHTMLV KQGDDYVYLP YPDPSRILGA GCFVDDIVKT DGTLMIERFV SLAIDAYPLT KHPNQEYADV FHLYLQYIR KLHDELTGHM LDMYSVMLTN DNTSRYWEPE FYEAMYTPHT VLQ UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #2: Non-structural protein 8
Macromolecule | Name: Non-structural protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.161445 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSSHHHHHH ENLYFQSNAA IASEFSSLPS YAAFATAQEA YEQAVANGDS EVVLKKLKKS LNVAKSEFDR DAAMQRKLEK MADQAMTQM YKQARSEDKR AKVTSAMQTM LFTMLRKLDN DALNNIINNA RDGCVPLNII PLTTAAKLMV VIPDYNTYKN T CDGTTFTY ...String: MGSSHHHHHH ENLYFQSNAA IASEFSSLPS YAAFATAQEA YEQAVANGDS EVVLKKLKKS LNVAKSEFDR DAAMQRKLEK MADQAMTQM YKQARSEDKR AKVTSAMQTM LFTMLRKLDN DALNNIINNA RDGCVPLNII PLTTAAKLMV VIPDYNTYKN T CDGTTFTY ASALWEIQQV VDADSKIVQL SEISMDNSPN LAWPLIVTAL RANSAVKLQ UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #3: Non-structural protein 7
Macromolecule | Name: Non-structural protein 7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 9.279776 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SNASKMSDVK CTSVVLLSVL QQLRVESSSK LWAQCVQLHN DILLAKDTTE AFEKMVSLLS VLLSMQGAVD INKLCEEMLD NRAT UniProtKB: Replicase polyprotein 1ab |
-Macromolecule #4: Product RNA
Macromolecule | Name: Product RNA / type: rna / ID: 4 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.242101 KDa |
Sequence | String: UUGGUCUCAA UACGGUAUGA GCCUACGCAG UA |
-Macromolecule #5: Template RNA
Macromolecule | Name: Template RNA / type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 10.539256 KDa |
Sequence | String: GG(7OK)ACUGCGU AGCUCAUACC GUAUUGAGAC CUU |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 373938 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |