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Yorodumi- PDB-3uyp: Crystal structure of the dengue virus serotype 4 envelope protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uyp | ||||||
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Title | Crystal structure of the dengue virus serotype 4 envelope protein domain III in complex with the variable domains of Mab 4E11 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / dengue antibody neutralization | ||||||
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 / membrane => GO:0016020 / 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 / endoplasmic reticulum membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Dengue virus 4 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Cockburn, J.J.B. / Navarro Sanchez, M.E. / Fretes, N. / Urvoas, A. / Staropoli, I. / Kikuti, C.M. / Coffey, L.L. / Arenzana Seisdedos, F. / Bedouelle, H. / Rey, F.A. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Mechanism of dengue virus broad cross-neutralization by a monoclonal antibody. Authors: Cockburn, J.J. / Navarro Sanchez, M.E. / Fretes, N. / Urvoas, A. / Staropoli, I. / Kikuti, C.M. / Coffey, L.L. / Arenzana Seisdedos, F. / Bedouelle, H. / Rey, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uyp.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uyp.ent.gz | 115.3 KB | Display | PDB format |
PDBx/mmJSON format | 3uyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/3uyp ftp://data.pdbj.org/pub/pdb/validation_reports/uy/3uyp | HTTPS FTP |
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-Related structure data
Related structure data | 3uzeC 3uzqSC 3uzvC 2h0pS 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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-Components
-Antibody / Protein , 2 types, 2 molecules AB
#1: Antibody | Mass: 27246.186 Da / Num. of mol.: 1 / Fragment: Single chain variable fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pLB1 / Production host: Escherichia coli (E. coli) / Strain (production host): HB2151 |
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#2: Protein | Mass: 12570.300 Da / Num. of mol.: 1 / Fragment: domain III (UNP residues 296-400) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 4 / Strain: Myanmar 1976 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9IZJ0, UniProt: Q2YHF0*PLUS |
-Non-polymers , 4 types, 285 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-TRS / | #6: 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: 2.92 Å3/Da / Density % sol: 57.83 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.7M ammonium sulphate, 12.5% glycerol, 0.1M TRIS-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 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: 1.999→47.193 Å / Num. all: 31933 / Num. obs: 31933 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 18.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H0P, 3UZQ Resolution: 2→47.19 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9321 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 138.35 Å2 / Biso mean: 39.3611 Å2 / Biso min: 9.5 Å2
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Refine analyze | Luzzati coordinate error obs: 0.234 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→47.19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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