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- EMDB-72778: Cryo-EM structure of MERS-CoV nsp10-nsp14 (E191A) in complex with... -

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Entry
Database: EMDB / ID: EMD-72778
TitleCryo-EM structure of MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA
Map dataDeepEMhancer-processed map
Sample
  • Complex: MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA
    • Protein or peptide: Replicase polyprotein 1ab
    • Protein or peptide: Guanine-N7 methyltransferase nsp14
    • RNA: T20P14-A RNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsMERS-CoV / exoribonuclease / proofreading / coronavirus / RNA / VIRAL PROTEIN / RNA-VIRAL PROTEIN complex
Function / homology
Function and homology information


host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / endonuclease activity / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / endonuclease activity / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / single-stranded RNA binding / regulation of autophagy / viral protein processing / lyase activity / host cell perinuclear region of cytoplasm / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / 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 / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Nonstructural protein 14, betacoronavirus / 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. ...RNA-dependent RNA polymerase, Middle East respiratory syndrome-related coronavirus / Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / AAA domain / Nonstructural protein 14, betacoronavirus / 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 / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Betacoronavirus single-stranded poly(A) binding domain / 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 / 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. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesMiddle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsYang Y / Liu C
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM150607 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP2AI177906 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural and catalytic diversity of coronavirus proofreading exoribonuclease.
Authors: Yu Li / Xiaocong Cao / Lauren M Recker / Yang Yang / Chang Liu /
Abstract: The coronavirus proofreading exoribonuclease (ExoN) is essential for genome fidelity and immune evasion of the viruses. Despite its critical roles in the viral life cycle, it is unclear how ExoNs ...The coronavirus proofreading exoribonuclease (ExoN) is essential for genome fidelity and immune evasion of the viruses. Despite its critical roles in the viral life cycle, it is unclear how ExoNs across different coronaviruses diverge in their structures and catalytic properties, which may lead to differences in viral genome mutation rates and, consequently, viral fitness, immune evasion, and resistance to antiviral drugs. Here, we present comparative structural and biochemical analyses of ExoNs between two most representative human coronaviruses, Middle East Respiratory Syndrome Coronavirus (MERS-CoV) from the merbecovirus subgenus and SARS-CoV-2 from the sarbecovirus subgenus. Our results reveal a markedly lower catalytic activity of ExoN from MERS-CoV than that from SARS-CoV-2. The molecular basis of such a divergence across the two coronaviruses is unveiled by the cryo-EM structures of MERS-CoV ExoN in complex with RNA substrates bearing different 3'-end base pairs or mismatch, which represent the first set of ExoN structures from a coronavirus outside the sarbecovirus subgenus. Our findings also identify two highly conserved structural determinants that dictate efficient excision of different nucleotides at the 3' terminus of RNA substrates by coronavirus ExoNs, a property that is pivotal for their roles in both viral RNA proofreading and immune evasion.
History
DepositionSep 19, 2025-
Header (metadata) releaseDec 24, 2025-
Map releaseDec 24, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72778.png

Downloads & links

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Map

FileDownload / File: emd_72778.map.gz / Format: CCP4 / Size: 129.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 324 pix.
= 303.037 Å		0.94 Å/pix.
x 324 pix.
= 303.037 Å		0.94 Å/pix.
x 324 pix.
= 303.037 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9353 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0266
Minimum - Maximum-0.0018012591 - 1.7919093
Average (Standard dev.)0.00034924454 (±0.01330191)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions324324324
Spacing324324324
CellA=B=C: 303.0372 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Raw map

Fileemd_72778_additional_1.map
AnnotationRaw map
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Additional map: Resolve density-modified map

Fileemd_72778_additional_2.map
AnnotationResolve density-modified map
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Half map: Half Map A

Fileemd_72778_half_map_1.map
AnnotationHalf Map A
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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72778_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA

EntireName: MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA
Components
  • Complex: MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA
    • Protein or peptide: Replicase polyprotein 1ab
    • Protein or peptide: Guanine-N7 methyltransferase nsp14
    • RNA: T20P14-A RNA
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA

SupramoleculeName: MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus

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Macromolecule #1: Replicase polyprotein 1ab

MacromoleculeName: Replicase polyprotein 1ab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 14.902897 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGSNTEFASN SSVLSLVNFT VDPQKAYLDF VNAGGAPLTN CVKMLTPKTG TGIAISVKPE STADQETYGG ASVCLYCRAH IEHPDVSGV CKYKGKFVQI PAQCVRDPVG FCLSNTPCNV CQYWIGYGCN CDSLRQAALP Q

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: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 59.190184 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SQIVTGLFKD CSRETSGLSP AYAPTYVSVD DKYKTSDELC VNLNLPANVP YSRVISRMGF KLDATVPGYP KLFITREEAV RQVRSWIGF DVEGAHASRN ACGTNVPLQL GFSTGVNFVV QPVGVVDTEW GNMLTGIAAR PPPGEQFKHL VPLMHKGAAW P IVRRRIVQ ...String:
SQIVTGLFKD CSRETSGLSP AYAPTYVSVD DKYKTSDELC VNLNLPANVP YSRVISRMGF KLDATVPGYP KLFITREEAV RQVRSWIGF DVEGAHASRN ACGTNVPLQL GFSTGVNFVV QPVGVVDTEW GNMLTGIAAR PPPGEQFKHL VPLMHKGAAW P IVRRRIVQ MLSDTLDKLS DYCTFVCWAH GFALTSASYF CKIGKEQKCC MCNRRAAAYS SPLQSYACWT HSCGYDYVYN PF FVDVQQW GYVGNLATNH DRYCSVHQGA HVASNDAIMT RCLAIHSCFI ERVDWDIEYP YISHEKKLNS CCRIVERNVV RAA LLAGSF DKVYDIGNPK GIPIVDDPVV DWHYFDAQPL TRKVQQLFYT EDMASRFADG LCLFWNCNVP KYPNNAIVCR FDTR VHSEF NLPGCDGGSL YVNKHAFHTP AYDVSAFRDL KPLPFFYYST TPCEVHGNGS MIEDIDYVPL KSAVCITACN LGGAV CRKH ATEYREYMEA YNLVSASGFR LWCYKTFDIY NLWSTFTKVQ

UniProtKB: Replicase polyprotein 1ab

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Macromolecule #3: T20P14-A RNA

MacromoleculeName: T20P14-A RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Molecular weightTheoretical: 12.517443 KDa
SequenceString:
GGGAAUGGGA UUUUAAUAGC UUCGGCUAUU AAAAUCCCA

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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
GridModel: Quantifoil R1.2/1.3 / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 296 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 43.03 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: NONE / Details: Ab-initio reconstructed using cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 302690
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9yck


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ycn:
Cryo-EM structure of MERS-CoV nsp10-nsp14 (E191A) in complex with T20P14-A RNA

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