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Yorodumi- PDB-2jqm: Yellow Fever Envelope Protein Domain III NMR Structure (S288-K398) -
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-Basic information
Entry | Database: PDB / ID: 2jqm | ||||||
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Title | Yellow Fever Envelope Protein Domain III NMR Structure (S288-K398) | ||||||
Components | Envelope protein E | ||||||
Keywords | TRANSFERASE / Yellow Fever Envelope Protein Domain III / Asibi strain | ||||||
Function / homology | Function and homology information flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / 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 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / 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 / 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 / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Yellow fever virus | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | Yellow Fever Envelope Protein Domain III NMR Structure (S288-K398) | ||||||
Authors | Volk, D.E. / Gandham, S.H. / May, F.J. / Anderson, A. / Barrett, A.D. / Gorenstein, D.G. | ||||||
Citation | Journal: Virology / Year: 2009 Title: Structure of yellow fever virus envelope protein domain III. Authors: Volk, D.E. / May, F.J. / Gandham, S.H. / Anderson, A. / Von Lindern, J.J. / Beasley, D.W. / Barrett, A.D. / Gorenstein, D.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jqm.cif.gz | 632.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jqm.ent.gz | 534.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/2jqm ftp://data.pdbj.org/pub/pdb/validation_reports/jq/2jqm | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11951.750 Da / Num. of mol.: 1 / Fragment: Envelope Protein Domain III / Mutation: L287M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yellow fever virus / Strain: Asibi Description: The N-terminal HIS tag of this vector was removed Production host: Escherichia coli (E. coli) / References: UniProt: Q6J3P1, UniProt: Q6DV88*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Yellow Fever Envelope Protein Domain III NMR Structure (S288-K398) |
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NMR experiment | Type: 3D 1H-15N NOESY |
-Sample preparation
Details | Contents: 50 mM NaCl, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 50 mM / Component: NaCl |
Sample conditions | Ionic strength: 0.05 / pH: 5.8 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 19 |