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- PDB-5ynb: Crystal structure of MERS-CoV nsp16/nsp10 complex bound to Sinefungin -

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Basic information

Entry
Database: PDB / ID: 5ynb
TitleCrystal structure of MERS-CoV nsp16/nsp10 complex bound to Sinefungin
Components
  • nsp10 protein
  • nsp16 protein
KeywordsTRANSFERASE / inhibitor / complex
Function / homology
Function and homology information


mRNA capping enzyme complex / host cell membrane / 7-methylguanosine mRNA capping / viral genome replication / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation ...mRNA capping enzyme complex / host cell membrane / 7-methylguanosine mRNA capping / viral genome replication / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / endonuclease activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / methyltransferase cap1 activity / 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 / single-stranded RNA binding / RNA helicase activity / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / 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 / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / zinc ion binding / ATP binding / identical protein 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 / Vaccinia Virus protein VP39 / 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. ...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 / Vaccinia Virus protein VP39 / 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 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. / 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
Similarity search - Domain/homology
SINEFUNGIN / ORF1ab polyprotein / ORF1a
Similarity search - Component
Biological speciesHuman betacoronavirus 2c EMC/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsWei, S.M. / Yang, L. / Ke, Z.H. / Chen, Y. / Guo, D.Y. / Fan, C.P.
Funding support China, 1items
OrganizationGrant numberCountry
NSFC31570762 China
CitationJournal: To Be Published
Title: Structural insights into the molecular mechanism of MERS Coronavirus RNA ribose 2'-O-methylation by nsp16/nsp10 protein complex
Authors: Wei, S.M. / Yang, L. / Ke, Z.H. / Liu, Q.Y. / Chen, Y. / Yang, Z.Z. / Guo, D.Y. / Fan, C.P.
History
DepositionOct 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nsp16 protein
B: nsp10 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1535
Polymers48,6402
Non-polymers5123
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-12 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.325, 70.206, 119.198
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-672-

HOH

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Components

#1: Protein nsp16 protein


Mass: 33737.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betacoronavirus 2c EMC/2012 / Gene: orf1ab / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K0BWD0
#2: Protein nsp10 protein


Mass: 14902.897 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betacoronavirus 2c EMC/2012 / Gene: orf1ab / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K4LC41
#3: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 5000 ME, 5% Tascimate, pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.98→48.23 Å / Num. obs: 79026 / % possible obs: 99.8 % / Redundancy: 10.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.026 / Rrim(I) all: 0.086 / Rsym value: 0.082 / Net I/σ(I): 19.4
Reflection shellHighest resolution: 1.98 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 3 / Num. unique obs: 3837 / CC1/2: 0.856 / Rsym value: 0.73 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r24

3r24


Resolution: 1.98→48.213 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.36
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2305 3757 5.02 %
Rwork0.1872 --
obs0.1893 74883 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.98→48.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 29 208 3364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113230
X-RAY DIFFRACTIONf_angle_d0.9014391
X-RAY DIFFRACTIONf_dihedral_angle_d4.7021924
X-RAY DIFFRACTIONf_chiral_restr0.056511
X-RAY DIFFRACTIONf_plane_restr0.005559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9787-2.00370.40831490.35892571X-RAY DIFFRACTION97
2.0037-2.03010.29971250.30612611X-RAY DIFFRACTION100
2.0301-2.05790.36081480.29472647X-RAY DIFFRACTION100
2.0579-2.08730.30711340.27742616X-RAY DIFFRACTION100
2.0873-2.11850.27971390.2422646X-RAY DIFFRACTION100
2.1185-2.15160.29311350.25122668X-RAY DIFFRACTION100
2.1516-2.18680.27851270.23952624X-RAY DIFFRACTION100
2.1868-2.22450.261610.24072626X-RAY DIFFRACTION100
2.2245-2.2650.28741420.23422624X-RAY DIFFRACTION100
2.265-2.30860.27491180.22062674X-RAY DIFFRACTION100
2.3086-2.35570.22071540.20522631X-RAY DIFFRACTION100
2.3557-2.40690.24891190.20052625X-RAY DIFFRACTION100
2.4069-2.46290.2391400.18442663X-RAY DIFFRACTION100
2.4629-2.52450.25161440.19072635X-RAY DIFFRACTION100
2.5245-2.59270.1731440.18592617X-RAY DIFFRACTION100
2.5927-2.6690.23211320.17562659X-RAY DIFFRACTION100
2.669-2.75520.21131370.19042624X-RAY DIFFRACTION100
2.7552-2.85360.24481490.17582620X-RAY DIFFRACTION100
2.8536-2.96790.1731320.17272663X-RAY DIFFRACTION100
2.9679-3.10290.2491450.17882646X-RAY DIFFRACTION100
3.1029-3.26650.22721370.1782622X-RAY DIFFRACTION100
3.2665-3.47110.19551370.16972645X-RAY DIFFRACTION100
3.4711-3.7390.2341410.16272637X-RAY DIFFRACTION100
3.739-4.11510.20611330.15622628X-RAY DIFFRACTION100
4.1151-4.71010.20421540.14682612X-RAY DIFFRACTION100
4.7101-5.93250.20531400.16612659X-RAY DIFFRACTION100
5.9325-48.22680.231410.19392633X-RAY DIFFRACTION100
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)
14.3323-0.92560.75513.7308-1.64354.43140.10360.3766-0.2571-0.2887-0.0061-0.15190.36430.0578-0.0970.17990.03350.03320.273-0.05890.263179.5061102.7826143.5735
23.45890.60690.44493.2837-0.12421.88740.07230.0555-0.6889-0.1359-0.0237-0.1120.541-0.1097-0.00540.3808-0.0242-0.06860.1825-0.01280.370267.311786.1408157.2777
34.12330.07790.32384.6575-1.51565.57980.09830.5522-0.2218-0.3969-0.17010.26080.7685-0.4177-0.00550.1697-0.0458-0.0760.2757-0.07280.295261.223195.8783149.4251
41.94450.3933-0.52141.1708-0.28832.39460.05810.1082-0.12520.0117-0.0366-0.11840.23070.0418-0.03510.16650.0121-0.0410.1569-0.03820.194870.6073100.2358152.3491
57.93493.8335.51955.20553.76797.4440.0493-0.2170.02340.2021-0.04920.56660.1911-0.4720.06640.2169-0.0240.01510.28750.02130.218260.3153102.4062170.5854
67.7614.53992.64144.34174.7757.0932-0.57480.98320.1829-1.08640.76990.8640.128-1.3415-0.13140.5328-0.10110.010.61770.05280.716558.05359.9316150.0905
72.61790.4860.75152.3962-0.44862.2714-0.1913-0.0356-0.3460.36090.0382-0.61520.11760.05820.13670.5426-0.0033-0.04380.23670.02480.667272.736967.9373158.2365
89.29551.64944.07732.162-0.38822.51970.5688-0.7641-0.13841.4228-0.43090.72170.0887-0.9288-0.16460.8184-0.11250.15460.45360.010.606960.116168.4153164.3697
97.1242-0.45710.73916.52640.12567.1175-0.2492-0.5169-0.83921.0748-0.1074-0.79590.61810.04160.32760.7043-0.0306-0.07270.26860.11140.774774.89764.0673164.0076
103.2161-0.1003-1.78216.01254.75994.77340.075-0.7613-0.86450.92690.3461-0.02370.95760.2365-0.36410.97970.0947-0.21730.47380.19690.782679.942459.2598170.6313
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 147 )
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 257 )
5X-RAY DIFFRACTION5chain 'A' and (resid 258 through 296 )
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 22 )
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 95 )
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 123 )
10X-RAY DIFFRACTION10chain 'B' and (resid 124 through 130 )

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