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Yorodumi- PDB-2px4: Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-... -
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-Basic information
Entry | Database: PDB / ID: 2px4 | ||||||
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Title | Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 2) | ||||||
Components | 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)] | ||||||
Keywords | TRANSFERASE / Murray Valley Encephalitis Virus / Methyltransferase / SAH / Structural Genomics / Oxford Protein Production Facility / OPPF | ||||||
Function / homology | Function and homology information 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / 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 / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Murray valley encephalitis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: J.Gen.Virol. / Year: 2007 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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Remark 600 | HETEROGEN AUTHORS STATE THAT THE UNKNOWN ATOMS UNX801-UNX809 MARK THE POSITION IN ELECTRON DENSITY ... HETEROGEN AUTHORS STATE THAT THE UNKNOWN ATOMS UNX801-UNX809 MARK THE POSITION IN ELECTRON DENSITY AND BELONG TO AN UNKNOWN CHEMICAL GROUP. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2px4.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2px4.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 2px4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/2px4 ftp://data.pdbj.org/pub/pdb/validation_reports/px/2px4 | HTTPS FTP |
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-Related structure data
Related structure data | 2px2SC 2px5C 2px8C 2pxaC 2pxcC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 30306.852 Da / Num. of mol.: 1 Fragment: NS5 2'-O Methyltransferase Domain: Residues 2530-2798 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Murray valley encephalitis virus (strain MVE-1-51) Genus: Flavivirus / Species: Murray Valley encephalitis virus / Strain: MVE-1-51, MVEV / Gene: NS5 / Plasmid: OPPF2936 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: P05769, RNA-directed RNA polymerase |
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-Non-polymers , 6 types, 201 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-UNX / #5: Chemical | ChemComp-SAH / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.6 M Magnesium sulfate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9765 Å |
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: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 13890 / % possible obs: 96.5 % / Observed criterion σ(I): -1.5 / Redundancy: 5.2 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1109 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PX2 Resolution: 2.2→26.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.128 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.218 / 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: 32.592 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→26.44 Å
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Refine LS restraints |
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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 / Origin x: 9.835 Å / Origin y: -0.077 Å / Origin z: 20.913 Å
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