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- PDB-5yn5: Crystal structure of MERS-CoV nsp10/nsp16 complex -

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Basic information

Entry
Database: PDB / ID: 5yn5
TitleCrystal structure of MERS-CoV nsp10/nsp16 complex
Components
  • nsp10 protein
  • nsp16 protein
KeywordsTRANSFERASE / 2'-O-MTase
Function / homology
Function and homology information


mRNA capping enzyme complex / 7-methylguanosine mRNA capping / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / viral genome replication / methyltransferase activity / : / methylation / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment ...mRNA capping enzyme complex / 7-methylguanosine mRNA capping / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / viral genome replication / methyltransferase activity / : / methylation / 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 / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease 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 / induction by virus of host autophagy / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding
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 / 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 / Non-structural protein NSP9, coronavirus / Non-structural protein NSP8, coronavirus
Similarity search - Domain/homology
ORF1ab polyprotein / ORF1a
Similarity search - Component
Biological speciesHuman betacoronavirus 2c EMC/2012
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 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 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)48,7714
Polymers48,6402
Non-polymers1312
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-11 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.754, 70.527, 119.254
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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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-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.89 Å3/Da / Density % sol: 57.38 %
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→48.5 Å / Num. obs: 82060 / % possible obs: 99.7 % / Redundancy: 10.9 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.019 / Rrim(I) all: 0.062 / Rsym value: 0.059 / Net I/σ(I): 24.7
Reflection shellHighest resolution: 1.96 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3961 / CC1/2: 0.886 / Rsym value: 0.692 / % possible all: 97.1

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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: 1.96→45.534 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.97
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2142 3774 4.85 %
Rwork0.1809 --
obs0.1825 77817 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→45.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3115 0 2 205 3322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113189
X-RAY DIFFRACTIONf_angle_d1.0124334
X-RAY DIFFRACTIONf_dihedral_angle_d3.2551880
X-RAY DIFFRACTIONf_chiral_restr0.064504
X-RAY DIFFRACTIONf_plane_restr0.006555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9605-1.98530.31781440.3572592X-RAY DIFFRACTION95
1.9853-2.01140.33221220.28482763X-RAY DIFFRACTION100
2.0114-2.0390.29791520.29222704X-RAY DIFFRACTION100
2.039-2.06810.31121300.27742808X-RAY DIFFRACTION100
2.0681-2.0990.29731530.25322720X-RAY DIFFRACTION100
2.099-2.13180.25811400.22932754X-RAY DIFFRACTION100
2.1318-2.16670.22911450.22692748X-RAY DIFFRACTION100
2.1667-2.20410.25871400.22252749X-RAY DIFFRACTION100
2.2041-2.24410.28291400.20752732X-RAY DIFFRACTION100
2.2441-2.28730.26851560.20652720X-RAY DIFFRACTION99
2.2873-2.3340.21260.20592744X-RAY DIFFRACTION100
2.334-2.38470.24921410.19912763X-RAY DIFFRACTION100
2.3847-2.44020.23461460.18722780X-RAY DIFFRACTION100
2.4402-2.50120.25811290.20082710X-RAY DIFFRACTION100
2.5012-2.56890.26431380.18092765X-RAY DIFFRACTION100
2.5689-2.64440.21291520.19112731X-RAY DIFFRACTION100
2.6444-2.72980.22981370.18552751X-RAY DIFFRACTION100
2.7298-2.82730.21741290.17992770X-RAY DIFFRACTION100
2.8273-2.94050.22211480.17192739X-RAY DIFFRACTION100
2.9405-3.07430.19221360.17642766X-RAY DIFFRACTION100
3.0743-3.23640.2641420.17942726X-RAY DIFFRACTION100
3.2364-3.43910.21811330.17112762X-RAY DIFFRACTION100
3.4391-3.70450.19651380.15242768X-RAY DIFFRACTION100
3.7045-4.07710.13181490.14612730X-RAY DIFFRACTION100
4.0771-4.66650.14281400.13442735X-RAY DIFFRACTION100
4.6665-5.87730.20441270.16532757X-RAY DIFFRACTION100
5.8773-45.54650.2241410.18932756X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 69.8288 Å / Origin y: 88.0929 Å / Origin z: 156.4696 Å
111213212223313233
T0.2582 Å2-0.0044 Å2-0.0659 Å2-0.2375 Å2-0.0107 Å2--0.2854 Å2
L1.2045 °20.3683 °2-0.1587 °2-1.9672 °20.1944 °2--0.6158 °2
S0.0418 Å °0.0239 Å °-0.3544 Å °0.089 Å °-0.034 Å °-0.1533 Å °0.2868 Å °-0.0819 Å °-0.003 Å °
Refinement TLS groupSelection details: all

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