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- PDB-2px8: Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-... -
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Basic information
Entry | Database: PDB / ID: 2px8 | ||||||
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Title | Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH and 7M-GTP | ||||||
![]() | Genome polyprotein [Contains: Capsid protein C (Core protein); Envelope protein M (Matrix protein); Major envelope protein E; Non-structural protein 1 (NS1); Non-structural protein 2A (NS2A); Flavivirin protease NS2B regulatory subunit; Flavivirin protease NS3 catalytic subunit; Non-structural protein 4A (NS4A); Non-structural protein 4B (NS4B); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5)] | ||||||
![]() | TRANSFERASE / Murray Valley Encephalitis Virus / Methyltransferase / SAH / 7M-GTP / 3PO / Structural Genomics / Oxford Protein Production Facility / OPPF | ||||||
Function / homology | ![]() flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Assenberg, R. / Ren, J. / Verma, A. / Walter, T.S. / Alderton, D. / Hurrelbrink, R.J. / Fuller, S.D. / Owens, R.J. / Stuart, D.I. / Grimes, J.M. / Oxford Protein Production Facility (OPPF) | ||||||
![]() | ![]() Title: Crystal structure of the Murray Valley encephalitis virus NS5 methyltransferase domain in complex with cap analogues. Authors: Assenberg, R. / Ren, J. / Verma, A. / Walter, T.S. / Alderton, D. / Hurrelbrink, R.J. / Fuller, S.D. / Bressanelli, S. / Owens, R.J. / Stuart, D.I. / Grimes, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.5 KB | Display | ![]() |
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PDB format | ![]() | 103.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.5 MB | Display | ![]() |
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Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 39.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2px2SC ![]() 2px4C ![]() 2px5C ![]() 2pxaC ![]() 2pxcC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 5 - 267 / Label seq-ID: 5 - 267
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30415.035 Da / Num. of mol.: 2 Fragment: NS5 2'-O Methyltransferase Domain: Residues 2530-2798 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Genus: Flavivirus / Species: Murray Valley encephalitis virus / Strain: MVE-1-51, MVEV / Gene: NS5 / Plasmid: OPPF2936 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 437 molecules ![](data/chem/img/MGT.gif)
![](data/chem/img/3PO.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/3PO.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium chloride, 0.1 M Bis-Tris pH 6.5, 25 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9535 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 29231 / % possible obs: 94.2 % / Observed criterion σ(I): -1.5 / Redundancy: 6 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2063 / % possible all: 68.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2PX2 Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.239 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS program has also been used in refinement
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.313 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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