+Open data
-Basic information
Entry | Database: PDB / ID: 5yn6 | ||||||
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Title | Crystal structure of MERS-CoV nsp10/nsp16 complex bound to SAM | ||||||
Components |
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Keywords | TRANSFERASE / complex | ||||||
Function / homology | Function and homology information mRNA capping enzyme complex / host cell membrane / 7-methylguanosine mRNA capping / 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 / host cell membrane / 7-methylguanosine mRNA capping / 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 / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / methylation / 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 / cysteine-type endopeptidase activity / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Human betacoronavirus 2c EMC/2012 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.947 Å | ||||||
Authors | Wei, S.M. / Yang, L. / Ke, Z.H. / Guo, D.Y. / Fan, C.P. | ||||||
Funding support | China, 1items
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Citation | Journal: 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. / Che, Y. / Yang, Z.Z. / Guo, D.Y. / Fan, C.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yn6.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yn6.ent.gz | 139.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yn6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yn6_validation.pdf.gz | 734.1 KB | Display | wwPDB validaton report |
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Full document | 5yn6_full_validation.pdf.gz | 738.4 KB | Display | |
Data in XML | 5yn6_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 5yn6_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/5yn6 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/5yn6 | HTTPS FTP |
-Related structure data
Related structure data | 5yn5C 5yn8C 5ynbC 5ynfC 5yniC 5ynjC 5ynmC 5ynnC 5ynoC 5ynpC 5ynqC 3r24S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: 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 | ||
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#2: 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-SAM / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.46 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 5000 ME, 5%Tascimate, pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9778 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→45.57 Å / Num. obs: 83890 / % possible obs: 99.5 % / Redundancy: 11.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.02 / Rrim(I) all: 0.068 / Rsym value: 0.065 / Net I/σ(I): 20.9 |
Reflection shell | Highest resolution: 1.95 Å / Redundancy: 11 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4132 / CC1/2: 0.888 / Rsym value: 0.739 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3r24 Resolution: 1.947→44.645 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.8 / Stereochemistry target values: ML Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.947→44.645 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 70.0151 Å / Origin y: 87.8646 Å / Origin z: 157.5553 Å
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Refinement TLS group | Selection details: all |