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- PDB-3uaj: Crystal structure of the envelope glycoprotein ectodomain from de... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uaj | ||||||
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Title | Crystal structure of the envelope glycoprotein ectodomain from dengue virus serotype 4 in complex with the fab fragment of the chimpanzee monoclonal antibody 5H2 | ||||||
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![]() | VIRAL PROTEIN/IMMUNE SYSTEM / dengue antibody membrane fusion / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() : / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase ...: / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / 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 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 / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Cockburn, J.J.B. / Stura, E.A. / Navarro-Sanchez, M.E. / Rey, F.A. | ||||||
![]() | ![]() Title: Structural insights into the neutralization mechanism of a higher primate antibody against dengue virus. Authors: Cockburn, J.J. / Navarro Sanchez, M.E. / Goncalvez, A.P. / Zaitseva, E. / Stura, E.A. / Kikuti, C.M. / Duquerroy, S. / Dussart, P. / Chernomordik, L.V. / Lai, C.J. / Rey, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 316.4 KB | Display | ![]() |
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PDB format | ![]() | 252 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.1 KB | Display | ![]() |
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Full document | ![]() | 501.8 KB | Display | |
Data in XML | ![]() | 51.7 KB | Display | |
Data in CIF | ![]() | 70.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3uc0C ![]() 1okeS 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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Unit cell |
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Components
#1: Protein | Mass: 47285.504 Da / Num. of mol.: 2 / Fragment: UNP residues 280-674 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | Mass: 25069.979 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Antibody | Mass: 23493.037 Da / Num. of mol.: 2 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #4: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 63.79 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion / pH: 7.5 Details: 8% PEG8000, 8% MPD, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2008 / Details: Dynamically bendable mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.232→47.738 Å / Num. all: 41087 / Num. obs: 39891 / % possible obs: 97.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 76.54 Å2 / Rsym value: 0.102 / Net I/σ(I): 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 54.31 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OKE Resolution: 3.232→47.738 Å / Cor.coef. Fo:Fc: 0.8535 / Cor.coef. Fo:Fc free: 0.8431 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.427 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 143.18 Å2 / Biso mean: 69.5232 Å2 / Biso min: 42.04 Å2
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Refine analyze | Luzzati coordinate error obs: 0.77 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.232→47.738 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.232→3.31 Å / Total num. of bins used: 20
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