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- EMDB-64956: Cryo-EM structure of SARS-CoV-2 nsp10/nsp14:RNA:SMP complex -

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Entry
Database: EMDB / ID: EMD-64956
TitleCryo-EM structure of SARS-CoV-2 nsp10/nsp14:RNA:SMP complex
Map data
Sample
  • Complex: SARS-CoV-2 nsp10/14:RNA-SMP
    • Protein or peptide: Non-structural protein 10
    • Protein or peptide: Guanine-N7 methyltransferase nsp14
    • RNA: RNA (28-MER)
  • RNA: RNA (26-MER)
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
KeywordsSARS-CoV-2 / exonuclease / nsp14 / nucleotide analogue / VIRAL PROTEIN/RNA / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / 3'-5'-RNA exonuclease activity / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / single-stranded 3'-5' DNA helicase activity / double-stranded DNA helicase activity / forked DNA-dependent helicase activity / four-way junction helicase activity / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 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
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.22 Å
AuthorsWang J / Lou Z / Liu D
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32188101 China
National Natural Science Foundation of China (NSFC)22477122 China
CitationJournal: J Am Chem Soc / Year: 2025
Title: Structural Basis and Rational Design of Nucleotide Analogue Inhibitor Evading the SARS-CoV-2 Proofreading Enzyme.
Authors: Junbo Wang / Yufan Pan / Yixiao Liu / Bo Huang / Ge Jin / Lejin Zhang / Feng Zhou / Xiaoyu Chang / Yucen Huang / Liming Yan / Yuanchen Dong / Zihe Rao / Dongsheng Liu / Zhiyong Lou /
Abstract: All coronaviruses (CoVs) encode an exoribonuclease in nonstructural protein nsp14 (nsp14 ExoN), which is required for the excision of mismatched nucleotides or nucleotide analogues (NAs) that are ...All coronaviruses (CoVs) encode an exoribonuclease in nonstructural protein nsp14 (nsp14 ExoN), which is required for the excision of mismatched nucleotides or nucleotide analogues (NAs) that are incorporated into nascent RNA. Here, we investigated the mechanism by which NAs evade SARS-CoV-2 nsp14 ExoN cleavage using chemically synthesized RNA with NAs incorporated at the 3' end. Nsp14 ExoN exhibited significantly attenuated activity on RNA with sofosbuvir monophosphate (SMP) compared with natural nucleotides, remdesivir/molnupiravir monophosphate, and, in particular, AT-9010 monophosphate (ATMP), which has the same chemically modified ribose moiety as SMP, incorporated at the 3' end. Cryo-electron microscopy structures of nsp10/14 bound to RNA-SMP/-ATMP and mutagenesis studies revealed the essential roles of H95/Q145/F146 in recognizing the base moiety and thus pulling the NAs into a favored conformation for cleavage. Therefore, NAs may evade nsp14 ExoN cleavage by having (1) a base that does not interact with H95, Q145, or F146 and (2) a chemically modified ribose. Guided by this hypothesis, two NAs were designed to effectively resist nsp14 ExoN cleavage. These results inform the rational design of anti-CoV NAs.
History
DepositionJun 6, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64956.png

Downloads & links

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Map

FileDownload / File: emd_64956.map.gz / Format: CCP4 / Size: 160.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 348 pix.
= 288.84 Å		0.83 Å/pix.
x 348 pix.
= 288.84 Å		0.83 Å/pix.
x 348 pix.
= 288.84 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.0927708 - 13.915126000000001
Average (Standard dev.)-0.026807282 (±0.30243123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions348348348
Spacing348348348
CellA=B=C: 288.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64956_half_map_1.map
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Half map: #2

Fileemd_64956_half_map_2.map
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Sample components

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Entire : SARS-CoV-2 nsp10/14:RNA-SMP

EntireName: SARS-CoV-2 nsp10/14:RNA-SMP
Components
  • Complex: SARS-CoV-2 nsp10/14:RNA-SMP
    • Protein or peptide: Non-structural protein 10
    • Protein or peptide: Guanine-N7 methyltransferase nsp14
    • RNA: RNA (28-MER)
  • RNA: RNA (26-MER)
  • Ligand: ZINC ION
  • Ligand: CALCIUM ION
  • Ligand: [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

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Supramolecule #1: SARS-CoV-2 nsp10/14:RNA-SMP

SupramoleculeName: SARS-CoV-2 nsp10/14:RNA-SMP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Macromolecule #1: Non-structural protein 10

MacromoleculeName: Non-structural protein 10 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 13.805737 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGNATEVPAN STVLSFCAFA VDAAKAYKDY LASGGQPITN CVKMLCTHTG TGQAITVTPE ANMDQESFGG ASCCLYCRCH IDHPNPKGF CDLKGKYVQI PTTCANDPVG FTLKNTVCTV CGMWKGYGCS CD

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #2: Guanine-N7 methyltransferase nsp14

MacromoleculeName: Guanine-N7 methyltransferase nsp14 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: mRNA (guanine-N7)-methyltransferase
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 59.316824 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ENVTGLFKDC SKVITGLHPT QAPTHLSVDT KFKTEGLCVD IPGIPKDMTY RRLISMMGFK MNYQVNGYPN MFITREEAIR HVRAWIGFD VEGCHATREA VGTNLPLQLG FSTGVNLVAV PTGYVDTPNN TDFSRVSAKP PPGDQFKHLI PLMYKGLPWN V VRIKIVQM ...String:
ENVTGLFKDC SKVITGLHPT QAPTHLSVDT KFKTEGLCVD IPGIPKDMTY RRLISMMGFK MNYQVNGYPN MFITREEAIR HVRAWIGFD VEGCHATREA VGTNLPLQLG FSTGVNLVAV PTGYVDTPNN TDFSRVSAKP PPGDQFKHLI PLMYKGLPWN V VRIKIVQM LSDTLKNLSD RVVFVLWAHG FELTSMKYFV KIGPERTCCL CDRRATCFST ASDTYACWHH SIGFDYVYNP FM IDVQQWG FTGNLQSNHD LYCQVHGNAH VASCDAIMTR CLAVHECFVK RVDWTIEYPI IGDELKINAA CRKVQHMVVK AAL LADKFP VLHDIGNPKA IKCVPQADVE WKFYDAQPCS DKAYKIEELF YSYATHSDKF TDGVCLFWNC NVDRYPANSI VCRF DTRVL SNLNLPGCDG GSLYVNKHAF HTPAFDKSAF VNLKQLPFFY YSDSPCESHG KQVVSDIDYV PLKSATCITR CNLGG AVCR HHANEYRLYL DAYNMMISAG FSLWVYKQFD TYNLWNTF

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #3: RNA (26-MER)

MacromoleculeName: RNA (26-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 8.217931 KDa
SequenceString:
UUCUCCUAAG AAGCUAUUAA AAUCAC

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Macromolecule #4: RNA (28-MER)

MacromoleculeName: RNA (28-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 8.967316 KDa
SequenceString:
AAGUGAUUUU AAUAGCUUCU UAGGAUGA

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #7: [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-y...

MacromoleculeName: [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-4-methyl-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
type: ligand / ID: 7 / Number of copies: 1 / Formula: K5X
Molecular weightTheoretical: 340.199 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 179937
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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