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- PDB-5ynp: Crystal structure of MERS-CoV nsp16/nsp10 complex bound to sinefu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ynp | ||||||
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Title | Crystal structure of MERS-CoV nsp16/nsp10 complex bound to sinefungin and m7GpppA | ||||||
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![]() | TRANSFERASE / complex / inhibitor | ||||||
Function / homology | ![]() mRNA capping enzyme complex / 7-methylguanosine mRNA capping / host cell membrane / viral genome replication / methyltransferase activity / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / 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 / 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wei, S.M. / Yang, L. / Ke, Z.H. / Guo, D.Y. / Fan, C.P. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.1 KB | Display | ![]() |
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PDB format | ![]() | 145.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yn5C ![]() 5yn6C ![]() 5yn8C ![]() 5ynbC ![]() 5ynfC ![]() 5yniC ![]() 5ynjC ![]() 5ynmC ![]() 5ynnC ![]() 5ynoC ![]() 5ynqC ![]() 3r24S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 33737.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 124 molecules ![](data/chem/img/SFG.gif)
![](data/chem/img/GTA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GTA.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SFG / | ||
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#4: Chemical | ChemComp-GTA / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 57.96 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 3, 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: 2.27→48.75 Å / Num. obs: 49298 / % possible obs: 99.8 % / Redundancy: 11 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.024 / Rrim(I) all: 0.081 / Rsym value: 0.077 / Net I/σ(I): 21.5 |
Reflection shell | Highest resolution: 2.27 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2637 / CC1/2: 0.895 / Rsym value: 0.593 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3r24 Resolution: 2.27→48.746 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.07 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→48.746 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: 71.2965 Å / Origin y: 87.6068 Å / Origin z: 156.556 Å
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Refinement TLS group | Selection details: all |