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- PDB-8f4y: Crystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex... -

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Basic information

Entry
Database: PDB / ID: 8f4y
TitleCrystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex with Compound 5a covalently bound to nsp16 and nsp10
Components
  • 2'-O-methyltransferase
  • Non-structural protein 10
KeywordsTRANSFERASE / CSBID / Structural Genomics / Center for Structural Biology of Infectious Diseases / nsp16-10 / 2'-O-Methyltransferase
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) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...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) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / 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 / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / 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
FORMIC ACID / Chem-XDU / Chem-XE0 / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Rosas-Lemus, M. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00035 United States
CitationJournal: Acs Infect Dis. / Year: 2023
Title: Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors.
Authors: Inniss, N.L. / Kozic, J. / Li, F. / Rosas-Lemus, M. / Minasov, G. / Rybacek, J. / Zhu, Y. / Pohl, R. / Shuvalova, L. / Rulisek, L. / Brunzelle, J.S. / Bednarova, L. / Stefek, M. / Kormanik, ...Authors: Inniss, N.L. / Kozic, J. / Li, F. / Rosas-Lemus, M. / Minasov, G. / Rybacek, J. / Zhu, Y. / Pohl, R. / Shuvalova, L. / Rulisek, L. / Brunzelle, J.S. / Bednarova, L. / Stefek, M. / Kormanik, J.M. / Andris, E. / Sebestik, J. / Li, A.S.M. / Brown, P.J. / Schmitz, U. / Saikatendu, K. / Chang, E. / Nencka, R. / Vedadi, M. / Satchell, K.J.F.
History
DepositionNov 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2'-O-methyltransferase
B: Non-structural protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,68620
Polymers48,7032
Non-polymers1,98418
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-35 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.040, 171.040, 52.029
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein 2'-O-methyltransferase / Non-structural protein 16 / nsp16


Mass: 33627.504 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 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): magic
References: UniProt: P0DTD1, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Protein Non-structural protein 10 / nsp10 / Growth factor-like peptide / GFL


Mass: 15075.190 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 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTD1

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Non-polymers , 6 types, 330 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-XDU / 4-[(E)-2-(2,4-dichlorophenyl)ethenyl]-6-(trifluoromethyl)pyrimidin-2-ol


Mass: 335.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H7Cl2F3N2O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-XE0 / 4-[2-(2,4-dichlorophenyl)ethyl]-6-(trifluoromethyl)pyrimidin-2-ol


Mass: 337.125 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H9Cl2F3N2O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.4 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 3.83 mg/ml (nsp10/nsp16 1:1), 0.15M Sodium chloride, 0.01M Tris pH 7.5 , 5% Glycerol; Screen: Anions (B2), 0.1M HEPES pH 7.5, 1.25M Sodium acetate; Soaks: Compound 5a, 24 hours; Cryo: 4M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 9, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.13→30 Å / Num. obs: 49128 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 42.2 Å2 / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.043 / Rrim(I) all: 0.113 / Rsym value: 0.104 / Χ2: 1.011 / Net I/σ(I): 17.5
Reflection shellResolution: 2.13→2.17 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 2485 / CC1/2: 0.718 / CC star: 0.914 / Rpim(I) all: 0.426 / Χ2: 0.998 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6w4h

6w4h


Resolution: 2.13→29.62 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 6.507 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1798 2374 4.9 %RANDOM
Rwork0.1573 ---
obs0.1584 46521 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167 Å2 / Biso mean: 52.305 Å2 / Biso min: 21.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å2-0 Å2
2--0.42 Å20 Å2
3----1.36 Å2
Refinement stepCycle: final / Resolution: 2.13→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 118 327 3597
Biso mean--84.04 54.73 -
Num. residues----408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123541
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163096
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.6734803
X-RAY DIFFRACTIONr_angle_other_deg2.4861.5747244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4215444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.2941011
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.42210580
X-RAY DIFFRACTIONr_chiral_restr0.0560.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024052
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02700
LS refinement shellResolution: 2.13→2.185 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 199 -
Rwork0.249 3372 -
all-3571 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.03510.15980.20861.28020.69922.1764-0.0291-0.17320.38220.15320.0243-0.0123-0.02580.14660.00480.1852-0.0077-0.0080.0387-0.05510.118894.87638.55234.372
21.7614-0.2333-0.05871.78730.31681.67760.00830.0281-0.132-0.14410.04890.13250.3093-0.103-0.05720.2534-0.0104-0.01930.0340.01320.023287.1221.02718.681
30.79290.39130.16631.34640.35742.13260.0019-0.13660.07410.15480.077-0.16810.27520.1941-0.07880.24450.0402-0.01560.0997-0.01380.066296.80826.57730.525
412.4008-5.2293-4.39343.44211.96152.20260.00240.22280.4387-0.20590.1587-0.18140.04050.035-0.16110.1682-0.00480.00710.07510.00960.016194.38229.3058.353
50.93831.4343-0.1186.6612-1.59141.6659-0.00480.1234-0.1653-0.226-0.0137-0.5260.19010.29750.01840.24890.04790.08240.1079-0.04260.0914104.4316.59212.482
613.115-2.5993-0.431414.20896.01212.6184-0.2091-0.49350.01650.38740.01550.60470.2416-0.11690.19360.2137-0.2149-0.07360.26670.13510.365157.5719.43816.971
73.5669-0.78390.3344.6697-0.21772.39880.14190.3068-0.2465-0.4054-0.02620.71850.3398-0.501-0.11570.1953-0.0719-0.10910.14760.00170.130271.31522.76111.782
87.0701-3.7153-2.520713.81228.25165.1095-0.16490.3037-0.9946-0.62360.11090.0879-0.03390.080.0540.8409-0.0278-0.10730.1757-0.2350.507973.5664.6587.281
94.2333-0.5187-0.1225.0077-0.73572.59440.08560.5025-0.7086-0.62390.05780.94980.5618-0.3645-0.14330.3308-0.1269-0.20530.1948-0.05470.315266.68919.4197.632
109.2426-4.6096.296811.34384.420811.22350.5030.5869-1.2622-0.7155-0.17411.0812-0.28790.3127-0.32890.2792-0.0425-0.2320.3573-0.04480.281960.50523.134-1.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6799 - 6827
2X-RAY DIFFRACTION2A6828 - 6926
3X-RAY DIFFRACTION3A6927 - 7042
4X-RAY DIFFRACTION4A7043 - 7061
5X-RAY DIFFRACTION5A7062 - 7096
6X-RAY DIFFRACTION6B4276 - 4289
7X-RAY DIFFRACTION7B4290 - 4332
8X-RAY DIFFRACTION8B4333 - 4344
9X-RAY DIFFRACTION9B4345 - 4375
10X-RAY DIFFRACTION10B4376 - 4385

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