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- PDB-9fwk: Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and i... -

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Entry
Database: PDB / ID: 9fwk
TitleEnsemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00123
Components
  • Guanine-N7 methyltransferase nsp14
  • Non-structural protein 10
KeywordsVIRAL PROTEIN / exoribonuclease / nsp10 / nsp14 / fragment screen
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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 / endonuclease activity ...viral genome replication / methyltransferase activity / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / 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 / endonuclease activity / 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 / methylation / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase activity / 5'-3' DNA helicase activity / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / 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 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lyase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / 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 / symbiont-mediated activation of host autophagy / viral translational frameshifting / 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
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 / Coronavirus Nsp6 transmembrane protein profile. / Coronavirus Nsp4 ectodomain (4Ecto) 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 / Carbamoyl-phosphate synthase subdomain signature 2. / : / Coronavirus replicase NSP2, N-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 Nsp3 ectodomain (3Ecto) profile.
Similarity search - Domain/homology
: / : / Replicase polyprotein 1a / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.509 Å
AuthorsKrojer, T. / Kozielski, F. / Sele, C. / Nyblom, M. / Fisher, S.Z. / Knecht, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis for small molecule binding to the SARS-CoV-2 nsp10-nsp14 ExoN complex.
Authors: Kozielski, F. / Fisher, S.Z. / Ma, S. / Al Busaidi, F. / Krupinska, E. / Nyblom, M. / Sele, C. / Sullivan, H.M. / Krojer, T. / Knecht, W.
History
DepositionJun 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 10
B: Guanine-N7 methyltransferase nsp14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2249
Polymers46,5602
Non-polymers6647
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.059, 99.711, 51.182
Angle α, β, γ (deg.)90, 114.73, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Non-structural protein 10 / nsp10 / Growth factor-like peptide / GFL


Mass: 13805.737 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli (E. coli) / References: UniProt: P0DTC1
#2: Protein Guanine-N7 methyltransferase nsp14 / Non-structural protein 14 / nsp14 / Proofreading exoribonuclease nsp14 / ExoN


Mass: 32753.783 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 (E. coli)
References: UniProt: P0DTD1, mRNA (guanine-N7)-methyltransferase, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters

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Non-polymers , 5 types, 371 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1IGT / (4S)-4-pyridin-4-ylpyrrolidin-2-one


Mass: 162.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-A1IGS / (4R)-4-pyridin-4-ylpyrrolidin-2-one


Mass: 162.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10N2O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Morpheus buffer 2 (pH: 7.5): 0.10M - Morpheus Ethylene glycols: 36.50%w/v Morpheus Amino acids: 0.11M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.509→46.49 Å / Num. obs: 62865 / % possible obs: 99.9 % / Redundancy: 6.93 % / CC1/2: 0.998 / Rmerge(I) obs: 0.0511 / Rpim(I) all: 0.021 / Rrim(I) all: 0.0553 / Net I/σ(I): 17.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalousRedundancy anomalous% possible all
4.096-46.4886.70.039544.162149021490320832080.997-0.0080.01650.04281.03997.83.4999.7
3.252-4.0966.840.037742.382155321553315231520.997-0.1620.01540.04080.88898.83.599.8
2.841-3.2526.990.041538.32203522035315331530.997-0.0970.01670.04480.955983.5999.9
2.581-2.8416.950.047633.772176221762312931290.997-0.060.01930.05140.97598.83.5499.9
2.396-2.5816.710.055829.242128221282317031700.996-0.0330.02320.06050.95498.53.4299.9
2.255-2.3966.830.062525.932152021520315031500.996-0.0930.02570.06770.90898.13.48100
2.142-2.2556.90.070323.12163521635313731370.9950.0220.02880.07610.90499.13.5100
2.049-2.1426.920.082319.982167421674313031300.993-0.1120.03380.0890.8698.23.53100
1.97-2.04970.097616.682197621976314031400.992-0.0430.03970.10550.82698.73.56100
1.902-1.977.020.12113.612197621976313031300.99-0.0340.04910.13070.80997.83.5999.9
1.842-1.9027.060.143711.562209122091312831280.9880.0170.05810.15520.7798.93.59100
1.79-1.8427.050.18268.982228222282316131610.9820.0040.07370.19720.724993.58100
1.742-1.796.980.21557.562201322013315331530.978-0.0230.08750.23290.6997.53.58100
1.7-1.7427.010.25656.512171421714309830980.970.0010.1040.27710.69498.43.56100
1.661-1.76.890.32095.192167221672314531450.9540.0170.13110.34710.66798.23.51100
1.626-1.6616.950.38154.342173621736312631260.94-0.020.15510.41230.64798.83.53100
1.593-1.6266.920.46373.682206722067319031900.914-0.0030.18870.50130.65397.73.54100
1.563-1.5936.940.53143.212145221452309130910.8780.0240.21610.57450.65697.43.56100
1.535-1.5636.920.6482.642165121651313031300.836-0.050.26370.70050.62997.73.54100
1.509-1.5356.970.73832.272191121911314431440.807-0.0170.29970.79780.633983.55100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata processing
XDSJan 10, 2022data reduction
Aimless0.7.7data scaling
TRUNCATE7.1.015data processing
DIMPLEphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.509→46.488 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.074 / SU Rfree Cruickshank DPI: 0.072
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 3046 -RANDOM
Rwork0.1829 ---
obs0.1837 62865 99.8 %-
Displacement parametersBiso mean: 30.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.8968 Å20 Å2-1.066 Å2
2--3.3931 Å20 Å2
3----1.4964 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.509→46.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 32 364 3608
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013359HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054570HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1117SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes568HARMONIC5
X-RAY DIFFRACTIONt_it3359HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion445SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3237SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.32
X-RAY DIFFRACTIONt_other_torsion14.96
LS refinement shellResolution: 1.51→1.52 Å
RfactorNum. reflection% reflection
Rfree0.2567 62 -
Rwork0.241 --
obs0.2417 1258 95.06 %

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