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- PDB-2px2: Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-... -
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Basic information
Entry | Database: PDB / ID: 2px2 | ||||||
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Title | Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 1) | ||||||
![]() | 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 / 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 | ![]() | 121.3 KB | Display | ![]() |
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PDB format | ![]() | 93.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 897.4 KB | Display | ![]() |
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Full document | ![]() | 902.8 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2px4C ![]() 2px5C ![]() 2px8C ![]() 2pxaC ![]() 2pxcC ![]() 1l9kS C: citing same article ( S: Starting model for refinement |
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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: ARG / Beg label comp-ID: ARG / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 5 / Auth seq-ID: 6 - 267 / Label seq-ID: 6 - 267
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Components
#1: Protein | Mass: 30306.852 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: ![]() ![]() #2: Chemical | ChemComp-CL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.5mM SAH, 0.2M Calcium chloride, 20% 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: Nov 30, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 31650 / % possible obs: 92.6 % / Observed criterion σ(I): -1.5 / Redundancy: 3.1 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2026 / % possible all: 60 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1L9K Resolution: 2→27.4 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.402 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.242 / 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: 34.372 Å2
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Refinement step | Cycle: LAST / Resolution: 2→27.4 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→2.052 Å / Total num. of bins used: 20
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