+Open data
-Basic information
Entry | Database: PDB / ID: 1oan | |||||||||
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Title | Crystal structure of the dengue 2 virus envelope protein | |||||||||
Components | ENVELOPE GLYCOPROTEIN | |||||||||
Keywords | GLYCOPROTEIN / DENGUE VIRUS / MEMBRANE FUSION / FLAVIVIRUS / FUSION PEPTIDE / LOW-PH CONFORMATIONAL CHANGE | |||||||||
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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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 | DENGUE VIRUS TYPE 2 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Modis, Y. / Harrison, S.C. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: A Ligand-Binding Pocket in the Dengue Virus Envelope Glycoprotein Authors: Modis, Y. / Ogata, S. / Clements, D. / Harrison, S.C. #1: Journal: Nature / Year: 1995 Title: The Envelope Glycoprotein from Tick-Borne Encephalitis Virus at 2 A Resolution Authors: Rey, F.A. / Heinz, F.X. / Mandl, C. / Kunz, C. / Harrison, S.C. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1oan.cif.gz | 170.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1oan.ent.gz | 135.1 KB | Display | PDB format |
PDBx/mmJSON format | 1oan.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1oan_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1oan_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1oan_validation.xml.gz | 35.2 KB | Display | |
Data in CIF | 1oan_validation.cif.gz | 47 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/1oan ftp://data.pdbj.org/pub/pdb/validation_reports/oa/1oan | HTTPS FTP |
-Related structure data
Related structure data | 1okeC 1oam C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.979, -0.2, -0.038), Vector: |
-Components
#1: Protein | Mass: 43819.391 Da / Num. of mol.: 2 / Fragment: SOLUBLE ECTODOMAIN, RESIDUES 281-674 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DENGUE VIRUS TYPE 2 / Strain: STRAIN PR159/S1 / Plasmid: PMTT / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P12823 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-NA / | #4: Sugar | #5: Water | ChemComp-HOH / | Sequence details | RESIDUES 100-108 FORM THE GLYCINE-RICH, HYDROPHOBIC FUSION PEPTIDE (ALLISON ET AL., J.VIROL. 75, ...RESIDUES 100-108 FORM THE GLYCINE-RICH, HYDROPHOBI | |
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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: 3.395 Å3/Da / Density % sol: 63 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 11% PEG 8000, 1 M NACL, 0.1 M TRIS/HCL PH 9.0, 20% GLYCEROL | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 27029 / % possible obs: 90.3 % / Redundancy: 10 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.5 / % possible all: 48.8 |
Reflection | *PLUS Highest resolution: 2.75 Å / Lowest resolution: 50 Å / % possible obs: 90 % / Rmerge(I) obs: 0.079 |
Reflection shell | *PLUS % possible obs: 49 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OAM 1oam Resolution: 2.75→48.1 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1691401.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.8907 Å2 / ksol: 0.360391 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→48.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.261 / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.261 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.54 / Rfactor Rwork: 0.478 |