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- PDB-8f4s: Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with C... -

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Basic information

Entry
Database: PDB / ID: 8f4s
TitleCrystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16
Components
  • 2'-O-methyltransferase
  • Non-structural protein 10
KeywordsTRANSFERASE / CSBID / Center for Structural Biology of Infectious Diseases / Methyl transferase / Structural Genomics
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 / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

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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)49,42211
Polymers48,7032
Non-polymers7199
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-23 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.847, 170.847, 51.881
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) / Strain (production host): BL21(DE3) / Variant (production host): magic / References: UniProt: P0DTD1

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Non-polymers , 5 types, 216 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / 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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4 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: 1.12705 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 2, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12705 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 47404 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 20.6 % / Biso Wilson estimate: 48 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.04 / Rrim(I) all: 0.183 / Rsym value: 0.178 / Χ2: 1.013 / Net I/σ(I): 24.4
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 21.2 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2327 / CC1/2: 0.575 / CC star: 0.855 / Rpim(I) all: 0.756 / Χ2: 1 / % 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: 2.15→29.59 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 7.352 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1909 2416 5.1 %RANDOM
Rwork0.1656 ---
obs0.1669 44897 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 207.74 Å2 / Biso mean: 60.406 Å2 / Biso min: 25.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.15 Å20 Å2
2--0.29 Å2-0 Å2
3----0.95 Å2
Refinement stepCycle: final / Resolution: 2.15→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 39 214 3396
Biso mean--79.21 60.64 -
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123340
X-RAY DIFFRACTIONr_bond_other_d0.0060.0162985
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.6454524
X-RAY DIFFRACTIONr_angle_other_deg0.431.5596974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0885421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.1851011
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.76110562
X-RAY DIFFRACTIONr_chiral_restr0.0570.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023781
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02657
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 148 -
Rwork0.276 3299 -
all-3447 -
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)
12.6060.71481.20821.81590.36562.3523-0.0496-0.19380.3670.06040.02740.09920.0028-0.06920.02220.15460.02130.01140.0413-0.02910.066887.968835.118130.4176
21.5686-0.1899-0.07443.0267-0.11092.09660.01740.1655-0.2375-0.17550.08550.09260.3569-0.0225-0.10290.304-0.0127-0.01470.0327-0.02120.043989.668117.607816.661
31.14010.21780.15841.87140.89012.5371-0.0253-0.14360.04870.15570.1284-0.18030.31360.228-0.10310.20180.0403-0.00780.0661-0.02370.022997.709425.846930.8456
44.6601-1.8563-1.11032.09050.84351.86040.16720.51580.2216-0.4494-0.06780.032-0.1378-0.126-0.09950.2196-0.0145-0.00240.07290.04080.031689.446532.228612.256
51.3011.8598-0.52627.1393-1.28421.6882-0.00260.137-0.1906-0.33630.0283-0.61610.1680.2972-0.02560.19810.04350.06050.0997-0.04090.083104.960116.588712.3905
612.5022-3.9352-4.616117.52139.64635.8349-0.4246-0.7541-0.74020.3540.25550.12120.27350.27660.16920.1264-0.099-0.01370.19110.11360.336856.9989.23617.3926
74.3504-0.4620.26135.0558-0.11863.59850.11780.4152-0.1652-0.4791-0.0570.68520.2728-0.4122-0.06080.1721-0.0458-0.11050.0998-0.00250.111571.494624.941211.3045
85.82631.7934-1.621611.3419-1.99748.3996-0.00670.773-1.0166-1.08040.16290.29641.117-0.3746-0.15620.3625-0.0588-0.14720.1214-0.11710.241973.23847.84789.7335
910.3669-2.3572-0.90355.40370.56692.32960.23720.3687-0.5347-0.4338-0.18020.8820.3801-0.1921-0.0570.1927-0.0637-0.1420.0628-0.00340.191865.176522.09512.3288
103.53351.3182-2.3925.6524-6.447410.8489-0.05510.3285-0.4784-0.3983-0.34150.28820.4585-0.05760.39660.1838-0.0549-0.07840.1503-0.11690.227764.254417.51071.897
114.7341-2.11086.66917.14932.311913.91320.24760.2607-0.2401-0.1996-0.26030.45150.22790.23120.01260.13540.0069-0.15550.1591-0.0670.210660.760322.6723-1.055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6799 - 6851
2X-RAY DIFFRACTION2A6852 - 6925
3X-RAY DIFFRACTION3A6926 - 7036
4X-RAY DIFFRACTION4A7037 - 7060
5X-RAY DIFFRACTION5A7061 - 7096
6X-RAY DIFFRACTION6B4276 - 4289
7X-RAY DIFFRACTION7B4290 - 4327
8X-RAY DIFFRACTION8B4328 - 4348
9X-RAY DIFFRACTION9B4349 - 4363
10X-RAY DIFFRACTION10B4364 - 4375
11X-RAY DIFFRACTION11B4376 - 4384

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