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- PDB-7v1e: Crystal structure of Omsk hemorrhagic fever virus NS5 MTase (in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7v1e | ||||||
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Title | Crystal structure of Omsk hemorrhagic fever virus NS5 MTase (in complex with SAH and m7GpppAmG) | ||||||
![]() | Core protein | ||||||
![]() | TRANSFERASE / Guanylyltransferase / methyltransferase / VIRAL PROTEIN | ||||||
Function / homology | ![]() symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jia, H. / Gong, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structures of Flavivirus NS5 Guanylyltransferase Reveal a GMP-Arginine Adduct. Authors: Jia, H. / Zhong, Y. / Peng, C. / Gong, 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 | ![]() | 78.3 KB | Display | ![]() |
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PDB format | ![]() | 54.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 20.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7fjtC ![]() 7v1bC ![]() 7v1cC ![]() 7v1dC ![]() 7v1fC ![]() 7v1gC ![]() 7v1hC ![]() 7v1iC ![]() 7v1jC ![]() 4k6mS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29948.389 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: C4TPE0, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase |
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-Non-polymers , 5 types, 209 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/V9G.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/V9G.gif)
![](data/chem/img/5GP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / |
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#3: Chemical | ChemComp-SAH / |
#4: Chemical | ChemComp-V9G / |
#5: Chemical | ChemComp-5GP / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.77 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 5.6 / Details: isopropanol, trisodium citrate, PEG 4000, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.59→50 Å / Num. obs: 37031 / % possible obs: 97.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.64 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.022 / Rrim(I) all: 0.046 / Χ2: 0.816 / Net I/σ(I): 13.3 / Num. measured all: 164089 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4K6M Resolution: 1.59→20.48 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 23.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.2 Å2 / Biso mean: 17.8158 Å2 / Biso min: 3.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.59→20.48 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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