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Yorodumi- PDB-4utb: Crystal structure of dengue 2 virus envelope glycoprotein in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4utb | |||||||||
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Title | Crystal structure of dengue 2 virus envelope glycoprotein in complex with the Fab fragment of the broadly neutralizing human antibody EDE2 A11 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN COMPLEX / VIRAL PROTEIN / MEMBRANE FUSION / CLASS 2 FUSION PROTEIN / DENGUE VIRUS / BROADLY NEUTRALIZING ANTIBODY / IMMUNE SYSTEM / FAB FRAGMENT | |||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / viral capsid / : / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / viral capsid / : / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 / protein dimerization activity / induction by virus of host autophagy / 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 / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | DENGUE VIRUS 2 HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.85 Å | |||||||||
Authors | Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Rey, F.A. | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Recognition Determinants of Broadly Neutralizing Human Antibodies Against Dengue Viruses. Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M. / Kikuti, C.M. / Sanchez, M.E.N. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M. / Kikuti, C.M. / Sanchez, M.E.N. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. / Petres, S. / Shepard, W.E. / Despres, P. / Arenzana-Seisdedos, F. / Dussart, P. / Mongkolsapaya, J. / Screaton, G.R. / Rey, F.A. #1: Journal: Nat Immunol / Year: 2015 Title: A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus. Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya ...Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya Duangchinda / Jonathan M Grimes / Wen-Yang Tsai / Chih-Yun Lai / Wei-Kung Wang / Prida Malasit / Jeremy Farrar / Cameron P Simmons / Z Hong Zhou / Felix A Rey / Juthathip Mongkolsapaya / Gavin R Screaton / Abstract: Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal ...Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal antibodies (mAbs) and identified a previously unknown epitope, the envelope dimer epitope (EDE), that bridges two envelope protein subunits that make up the 90 repeating dimers on the mature virion. The mAbs to EDE were broadly reactive across the dengue serocomplex and fully neutralized virus produced in either insect cells or primary human cells, with 50% neutralization in the low picomolar range. Our results provide a path to a subunit vaccine against dengue virus and have implications for the design and monitoring of future vaccine trials in which the induction of antibody to the EDE should be prioritized. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4utb.cif.gz | 331 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4utb.ent.gz | 266 KB | Display | PDB format |
PDBx/mmJSON format | 4utb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/4utb ftp://data.pdbj.org/pub/pdb/validation_reports/ut/4utb | HTTPS FTP |
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-Related structure data
Related structure data | 4ut6C 4ut7C 4ut9C 4utaC 4utcC 3h0tS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46816.547 Da / Num. of mol.: 2 / Fragment: SOLUBLE ECTODOMAIN, RESIDUES 281-671 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DENGUE VIRUS 2 / Strain: FGA-02 / Plasmid: PMT/BIP/V5-HIS / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q68Y26, UniProt: A0A0B4SHY9*PLUS |
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-Antibody , 2 types, 4 molecules HILM
#2: Antibody | Mass: 30355.521 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT HEAVY CHAIN, RESIDUES 1-263 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: SEE SECONDARY REFERENCE / Cell: B LYMPHOCYTE / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) #3: Antibody | Mass: 23107.664 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT LIGHT CHAIN, RESIDUES -1-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: SEE SECONDARY REFERENCE / Cell: B LYMPHOCYTE / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) |
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-Sugars , 3 types, 4 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 5 molecules
#7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE RESIDUES AFTER W391 DERIVE FROM THE VECTOR. THE RESIDUES ARE NUMBERED FROM 1392. RESIDUES 1392 ...THE RESIDUES AFTER W391 DERIVE FROM THE VECTOR. THE RESIDUES ARE NUMBERED FROM 1392. RESIDUES 1392 TO 1394 COMPLETE THE G STRAND OF ENVELOPE GLYCOPROTE |
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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: 2.82 Å3/Da / Density % sol: 0.56 % / Description: NONE |
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Crystal grow | Details: 100MM HEPES PH 7.5 10% (W/V) PEG 6,000 5% (V/V) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.000002 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000002 Å / Relative weight: 1 |
Reflection | Resolution: 3.85→50 Å / Num. obs: 21168 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.83 % / Biso Wilson estimate: 68.58 Å2 / Rmerge(I) obs: 0.27 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3.85→4.22 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.4 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H0T Resolution: 3.85→20 Å / Cor.coef. Fo:Fc: 0.859 / Cor.coef. Fo:Fc free: 0.8411 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.759
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Displacement parameters | Biso mean: 129.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.987 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.85→4.04 Å / Total num. of bins used: 11
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