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- PDB-5ynq: Crystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH an... -

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Basic information

Entry
Database: PDB / ID: 5ynq
TitleCrystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppG
Components
  • nsp10 protein
  • nsp16 protein
KeywordsTRANSFERASE / complex / inhibitor
Function / homology
Function and homology information


mRNA capping enzyme complex / 7-methylguanosine mRNA capping / host cell membrane / viral genome replication / methyltransferase activity / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation ...mRNA capping enzyme complex / 7-methylguanosine mRNA capping / host cell membrane / viral genome replication / methyltransferase activity / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / RNA helicase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / virus-mediated perturbation of host defense response / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding / cytoplasm
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 / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain ...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 / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / 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 Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Coronavirus 3Ecto domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus
Similarity search - Domain/homology
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / S-ADENOSYL-L-HOMOCYSTEINE / ORF1ab polyprotein / ORF1a
Similarity search - Component
Biological speciesHuman betacoronavirus 2c EMC/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.958 Å
AuthorsWei, S.M. / Yang, L. / Ke, Z.H. / 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. / Yang, Z.Z. / Chen, Y. / Guo, D.Y. / Fan, C.P.
History
DepositionOct 25, 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)49,9596
Polymers48,6402
Non-polymers1,3194
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-16 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.874, 70.101, 118.937
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-640-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 171 molecules

#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O18P3
#5: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 5000 ME, 5% Tascimate

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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: 1.96→48.4 Å / Num. obs: 81914 / % possible obs: 99.8 % / Redundancy: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.019 / Rrim(I) all: 0.06 / Rsym value: 0.057 / Net I/σ(I): 22.3
Reflection shellHighest resolution: 1.96 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3576 / CC1/2: 0.843 / Rsym value: 0.76 / % possible all: 99.2

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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: 1.958→45.349 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.97 / Stereochemistry target values: ML
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2165 3794 4.89 %
Rwork0.1863 --
obs0.1878 77662 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.958→45.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 80 167 3393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043306
X-RAY DIFFRACTIONf_angle_d1.214503
X-RAY DIFFRACTIONf_dihedral_angle_d8.0042011
X-RAY DIFFRACTIONf_chiral_restr0.145521
X-RAY DIFFRACTIONf_plane_restr0.004564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9579-1.98270.55471530.39442626X-RAY DIFFRACTION97
1.9827-2.00870.32041300.33052769X-RAY DIFFRACTION100
2.0087-2.03630.30991300.3242722X-RAY DIFFRACTION100
2.0363-2.06540.34951540.29712788X-RAY DIFFRACTION100
2.0654-2.09620.31671150.27692726X-RAY DIFFRACTION100
2.0962-2.12890.34091610.25142734X-RAY DIFFRACTION100
2.1289-2.16380.2621340.25562763X-RAY DIFFRACTION100
2.1638-2.20120.27021460.23042727X-RAY DIFFRACTION100
2.2012-2.24120.29831480.22982710X-RAY DIFFRACTION100
2.2412-2.28430.21821190.22082725X-RAY DIFFRACTION99
2.2843-2.33090.2661440.21682738X-RAY DIFFRACTION100
2.3309-2.38160.22811350.20792759X-RAY DIFFRACTION100
2.3816-2.4370.21051500.19772716X-RAY DIFFRACTION100
2.437-2.49790.23951410.19932745X-RAY DIFFRACTION100
2.4979-2.56550.24561580.20552749X-RAY DIFFRACTION100
2.5655-2.64090.24851260.20912726X-RAY DIFFRACTION100
2.6409-2.72620.23221570.20692721X-RAY DIFFRACTION100
2.7262-2.82360.25921350.19392754X-RAY DIFFRACTION100
2.8236-2.93660.22111460.18082736X-RAY DIFFRACTION100
2.9366-3.07020.2081520.18162731X-RAY DIFFRACTION100
3.0702-3.23210.19761370.1862720X-RAY DIFFRACTION100
3.2321-3.43450.21161290.17662769X-RAY DIFFRACTION100
3.4345-3.69960.14911420.1552755X-RAY DIFFRACTION100
3.6996-4.07170.1981370.1492735X-RAY DIFFRACTION100
4.0717-4.66030.1581460.13552731X-RAY DIFFRACTION100
4.6603-5.86950.18861480.15582732X-RAY DIFFRACTION100
5.8695-45.3610.21431210.18552761X-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)
13.2719-0.37330.75555.7032-2.17215.46490.19380.5486-0.09-0.452-0.1144-0.23380.26630.0801-0.06330.24350.04180.04510.3365-0.06860.261380.5277103.9055144.2855
23.29441.3768-1.70311.6839-1.86674.1240.18430.3703-0.8347-0.8672-0.283-0.06011.3250.5327-0.0350.51170.102-0.03680.5348-0.260.657880.621885.7286140.9445
33.94910.9458-0.96883.4985-0.60380.870.10050.0654-0.6161-0.0916-0.0322-0.18660.4982-0.0187-0.07290.39650.0038-0.13090.2174-0.02030.34971.486889.2995157.5424
44.68040.5179-0.10944.1493-0.21411.83030.23990.0837-1.00930.0527-0.0040.09320.5825-0.2657-0.21480.5219-0.0771-0.10510.2596-0.00590.506264.259883.1735158.6508
53.36560.7881.88353.70841.15336.35260.1760.2156-0.4715-0.1593-0.09450.32290.3419-0.4686-0.06050.3203-0.0579-0.0710.312-0.06320.335759.805292.7556152.5893
63.86940.0397-1.34863.9797-0.18485.510.18890.7174-0.0439-0.4896-0.03970.1880.4557-0.6499-0.10240.29680.0139-0.11190.4924-0.03880.297559.2096100.1604145.4445
73.3316-0.0081-1.11450.8765-0.2773.55880.1090.31510.0254-0.04860.0066-0.03990.0919-0.0523-0.11320.24210.0207-0.03750.2398-0.03250.201370.2487103.3331150.0601
83.9295-1.2092-0.67583.3036-1.10241.36090.0393-0.1921-0.7467-0.0422-0.0875-0.43360.72150.55340.04330.33230.0271-0.15960.261-0.06770.473983.353390.1163157.6626
95.96752.10943.68086.81113.61997.8878-0.0149-0.1590.04990.2966-0.07370.6140.1939-0.48060.09840.3189-0.0302-0.01530.39920.02620.215462.1416102.8871171.2721
106.5822-1.64542.28194.07394.50838.24150.3760.4336-0.2588-1.07030.55650.2034-0.554-0.5006-0.69380.786-0.16250.12750.5064-0.17020.921459.000959.8412149.5624
111.09171.9911.04265.8381.55260.9576-0.24970.0163-0.6496-0.6547-0.0161-0.4985-0.09340.15360.26530.697-0.0584-0.00450.3309-0.10831.07869.133260.5843151.1564
122.0241-0.90191.42260.6864-1.4473.2156-0.583-0.4198-0.6540.40920.0644-1.05870.0301-0.17280.50320.83330.0885-0.34560.35810.10.904582.633975.2766163.4958
132.5068-1.95181.34841.6228-1.17772.61920.1609-0.1653-0.90250.7226-0.089-0.88070.40810.0536-0.10970.7477-0.0218-0.24330.31640.08480.986877.59172.2105162.6028
146.24580.6356-2.00766.9248-0.64025.86560.0703-0.0742-0.7401-0.13140.1617-0.1464-0.2809-0.5321-0.18650.6304-0.0527-0.03250.3602-0.04940.795760.413866.9576157.083
150.0614-0.0148-0.0280.00250.00570.0108-0.0998-0.8835-0.22091.1950.11750.24540.782-0.176-0.00570.998-0.13010.10190.57370.15060.839257.981464.6413168.1083
162.32290.6429-1.23427.76133.18162.28250.2362-0.7128-0.23740.523-0.7119-0.28240.6159-0.13960.59720.7911-0.0768-0.05660.38860.07440.594265.528671.1474165.3088
172.9322-0.27080.65894.77570.7932.1196-0.1932-0.0891-1.02920.7860.1139-0.82950.35140.1786-0.02240.741-0.0374-0.11420.31210.01491.225775.588463.7518159.7004
189.53022.7437-1.23194.1112.02735.9494-0.1138-0.21410.32130.1976-0.3109-0.98020.1301-0.52540.38611.46620.0424-0.32010.63410.28131.063775.957263.8005174.4068
197.79560.8692-2.4745.76033.27443.01210.1627-0.7724-0.58770.2536-0.0644-0.19370.45980.3981-0.08151.07710.1652-0.25980.58950.251.246680.10859.9659169.4917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 114 )
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 137 )
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 159 )
7X-RAY DIFFRACTION7chain 'A' and (resid 160 through 234 )
8X-RAY DIFFRACTION8chain 'A' and (resid 235 through 257 )
9X-RAY DIFFRACTION9chain 'A' and (resid 258 through 293 )
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 22 )
11X-RAY DIFFRACTION11chain 'B' and (resid 23 through 43 )
12X-RAY DIFFRACTION12chain 'B' and (resid 44 through 53 )
13X-RAY DIFFRACTION13chain 'B' and (resid 54 through 73 )
14X-RAY DIFFRACTION14chain 'B' and (resid 74 through 83 )
15X-RAY DIFFRACTION15chain 'B' and (resid 84 through 88 )
16X-RAY DIFFRACTION16chain 'B' and (resid 89 through 95 )
17X-RAY DIFFRACTION17chain 'B' and (resid 96 through 117 )
18X-RAY DIFFRACTION18chain 'B' and (resid 118 through 122 )
19X-RAY DIFFRACTION19chain 'B' and (resid 123 through 130 )

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