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Yorodumi- PDB-4gsx: High resolution structure of dengue virus serotype 1 sE containin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gsx | ||||||
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Title | High resolution structure of dengue virus serotype 1 sE containing stem | ||||||
Components | Envelope protein E | ||||||
Keywords | VIRAL PROTEIN / Viral Fusion Protein | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å | ||||||
Authors | Klein, D.E. / Choi, J.L. / Harrison, S.C. | ||||||
Citation | Journal: J.Virol. / Year: 2013 Title: Structure of a dengue virus envelope protein late-stage fusion intermediate. Authors: Klein, D.E. / Choi, J.L. / Harrison, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gsx.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gsx.ent.gz | 140.4 KB | Display | PDB format |
PDBx/mmJSON format | 4gsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/4gsx ftp://data.pdbj.org/pub/pdb/validation_reports/gs/4gsx | HTTPS FTP |
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-Related structure data
Related structure data | 4gt0C 3g7tS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 46796.188 Da / Num. of mol.: 2 / Fragment: UNP residues 281-691 / Mutation: W101H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 1 / Strain: WP74 / Gene: Envelope Protein / Plasmid: pFastBac / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: P17763 #2: Sugar | #3: Chemical | ChemComp-CD / #4: Chemical | ChemComp-CL / | #5: 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: 2.71 Å3/Da / Density % sol: 54.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2011 / Details: mirrors |
Radiation | Monochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection twin | Type: merohedral / Operator: h,-h-k,-l / Fraction: 0.4 |
Reflection | Resolution: 1.9→50 Å / Num. all: 76924 / Num. obs: 76924 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 1.84 / Num. unique all: 7595 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3G7T Resolution: 1.903→29.13 Å / σ(F): 1.4 / Phase error: 28.8 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.903→29.13 Å
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Refine LS restraints |
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LS refinement shell |
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