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Yorodumi- PDB-2r69: Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue v... -
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-Basic information
Entry | Database: PDB / ID: 2r69 | ||||||
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Title | Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom resolution | ||||||
Components |
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Keywords | viral protein/Immune system / Fab-antigen complex / Capsid protein / Cleavage on pair of basic residues / Core protein / Envelope protein / Glycoprotein / Membrane / Transmembrane / Virion / viral protein-Immune system COMPLEX | ||||||
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 / viral nucleocapsid / 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 innate immune response / 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 2 Thailand/16681/84 Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å | ||||||
Authors | Lok, S.M. / Kostyuchenko, V.K. / Nybakken, G.E. / Holdaway, H.A. / Battisti, A.J. / Sukupolvi-petty, S. / Sedlak, D. / Fremont, D.H. / Chipman, P.R. / Roehrig, J.T. ...Lok, S.M. / Kostyuchenko, V.K. / Nybakken, G.E. / Holdaway, H.A. / Battisti, A.J. / Sukupolvi-petty, S. / Sedlak, D. / Fremont, D.H. / Chipman, P.R. / Roehrig, J.T. / Diamond, M.S. / Kuhn, R.J. / Rossmann, M.G. | ||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2008 Title: Binding of a neutralizing antibody to dengue virus alters the arrangement of surface glycoproteins. Authors: Shee-Mei Lok / Victor Kostyuchenko / Grant E Nybakken / Heather A Holdaway / Anthony J Battisti / Soila Sukupolvi-Petty / Dagmar Sedlak / Daved H Fremont / Paul R Chipman / John T Roehrig / ...Authors: Shee-Mei Lok / Victor Kostyuchenko / Grant E Nybakken / Heather A Holdaway / Anthony J Battisti / Soila Sukupolvi-Petty / Dagmar Sedlak / Daved H Fremont / Paul R Chipman / John T Roehrig / Michael S Diamond / Richard J Kuhn / Michael G Rossmann / Abstract: The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding ...The monoclonal antibody 1A1D-2 has been shown to strongly neutralize dengue virus serotypes 1, 2 and 3, primarily by inhibiting attachment to host cells. A crystal structure of its antigen binding fragment (Fab) complexed with domain III of the viral envelope glycoprotein, E, showed that the epitope would be partially occluded in the known structure of the mature dengue virus. Nevertheless, antibody could bind to the virus at 37 degrees C, suggesting that the virus is in dynamic motion making hidden epitopes briefly available. A cryo-electron microscope image reconstruction of the virus:Fab complex showed large changes in the organization of the E protein that exposed the epitopes on two of the three E molecules in each of the 60 icosahedral asymmetric units of the virus. The changes in the structure of the viral surface are presumably responsible for inhibiting attachment to cells. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r69.cif.gz | 94.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r69.ent.gz | 73.4 KB | Display | PDB format |
PDBx/mmJSON format | 2r69.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r69_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 2r69_full_validation.pdf.gz | 511.6 KB | Display | |
Data in XML | 2r69_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | 2r69_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r6/2r69 ftp://data.pdbj.org/pub/pdb/validation_reports/r6/2r69 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10932.665 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 Thailand/16681/84 / Genus: Flavivirus / Species: Dengue virus / Strain: 16681 / Gene: E protein / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18356, UniProt: P29990*PLUS |
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#2: Antibody | Mass: 22926.557 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balbc / Gene: immunoglobulin / Cell line (production host): hybridoma |
#3: Antibody | Mass: 23412.869 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Strain: balbc / Gene: immunoglobulin / Cell line (production host): hybridoma |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 12% PEG 3350, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→50 Å / Num. obs: 6433 / % possible obs: 68.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.118 / Χ2: 1.226 / Net I/σ(I): 8 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.219 / Num. unique all: 352 / Χ2: 1.123 / % possible all: 37.4 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.458 / Cor.coef. Fo:Fc: 0.31
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→20 Å / σ(F): 0
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Solvent computation | Bsol: 10 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.789 Å2
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Refinement step | Cycle: LAST / Resolution: 3.8→20 Å
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Xplor file | Serial no: 1 / Param file: CNS_TOPPAR:protein_rep.param |