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

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Basic information

Entry
Database: PDB / ID: 5yno
TitleCrystal structure of MERS-CoV nsp16/nsp10 complex bound to SAH and m7GpppA
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 suppression of host NF-kappaB cascade / symbiont-mediated degradation of host mRNA ...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 suppression of host NF-kappaB cascade / 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 / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / methylation / cysteine-type deubiquitinase activity / RNA helicase activity / host cell perinuclear region of cytoplasm / single-stranded RNA binding / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane / 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 / 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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface 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 / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / 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. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus
Similarity search - Domain/homology
Chem-GTA / S-ADENOSYL-L-HOMOCYSTEINE / 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. / 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)49,9436
Polymers48,6402
Non-polymers1,3034
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-15 kcal/mol
Surface area17760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.193, 70.186, 119.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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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, 187 molecules

#3: Chemical ChemComp-SAH / 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-GTA / P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE / 7-METHYL-GPPPA


Mass: 787.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N10O17P3
#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


Mass: 18.015 Da / Num. of mol.: 183 / 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: 57.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / 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→48.55 Å / Num. obs: 82216 / % possible obs: 99.8 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 21.3
Reflection shellHighest resolution: 1.96 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4028 / CC1/2: 0.896 / Rsym value: 0.705 / % possible all: 99.3

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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→48.536 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.25
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2272 3799 4.87 %
Rwork0.1927 --
obs0.1944 78000 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.96→48.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 79 183 3419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013316
X-RAY DIFFRACTIONf_angle_d0.964514
X-RAY DIFFRACTIONf_dihedral_angle_d7.9192011
X-RAY DIFFRACTIONf_chiral_restr0.058522
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9615-1.98640.34111510.36242679X-RAY DIFFRACTION98
1.9864-2.01250.34391340.30632754X-RAY DIFFRACTION100
2.0125-2.04010.27161250.30242769X-RAY DIFFRACTION100
2.0401-2.06920.40361540.38342764X-RAY DIFFRACTION100
2.0692-2.10010.46831370.37552734X-RAY DIFFRACTION100
2.1001-2.13290.31571400.24792776X-RAY DIFFRACTION100
2.1329-2.16790.26111420.24152767X-RAY DIFFRACTION100
2.1679-2.20530.23561310.22032715X-RAY DIFFRACTION100
2.2053-2.24540.32481700.28682745X-RAY DIFFRACTION100
2.2454-2.28860.36911050.31782724X-RAY DIFFRACTION99
2.2886-2.33530.21971770.22162763X-RAY DIFFRACTION100
2.3353-2.38610.26191160.1982751X-RAY DIFFRACTION100
2.3861-2.44160.27081350.19222765X-RAY DIFFRACTION100
2.4416-2.50260.17641480.19482746X-RAY DIFFRACTION100
2.5026-2.57030.22591450.18122749X-RAY DIFFRACTION100
2.5703-2.64590.25161400.19622741X-RAY DIFFRACTION100
2.6459-2.73130.29841400.2022749X-RAY DIFFRACTION100
2.7313-2.82890.22451400.20282753X-RAY DIFFRACTION100
2.8289-2.94220.23911460.18862758X-RAY DIFFRACTION100
2.9422-3.0760.22491400.182741X-RAY DIFFRACTION100
3.076-3.23820.27161390.18112738X-RAY DIFFRACTION100
3.2382-3.4410.26671370.17792772X-RAY DIFFRACTION100
3.441-3.70660.15231440.16012752X-RAY DIFFRACTION100
3.7066-4.07940.17561510.15132738X-RAY DIFFRACTION100
4.0794-4.66930.1681370.14022745X-RAY DIFFRACTION100
4.6693-5.88130.18341340.16132750X-RAY DIFFRACTION100
5.8813-48.55110.21851410.19132763X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 70.4212 Å / Origin y: 88.0054 Å / Origin z: 155.9791 Å
111213212223313233
T0.2986 Å2-0.0033 Å2-0.0829 Å2-0.2453 Å2-0.0424 Å2--0.3213 Å2
L1.567 °20.3842 °2-0.2311 °2-2.2643 °20.3135 °2--0.6321 °2
S0.0275 Å °0.0788 Å °-0.4805 Å °0.1246 Å °-0.019 Å °-0.1959 Å °0.2657 Å °-0.07 Å °-0.0044 Å °
Refinement TLS groupSelection details: all

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