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Yorodumi- PDB-5n09: Crystal structure of L107C/A313C covalently linked dengue 2 virus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n09 | |||||||||
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Title | Crystal structure of L107C/A313C covalently linked dengue 2 virus envelope glycoprotein dimer 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 / FAB FRAGMENT | |||||||||
Function / homology | Function and homology information flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / 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 / viral RNA genome replication / serine-type endopeptidase activity / 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 / 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: 3.9 Å | |||||||||
Authors | Duquerroy, S. / Rouvinski, A. / Guardado-Calvo, P. / Vaney, M.-C. / Sharma, A. / Rey, F. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nat Commun / Year: 2017 Title: Covalently linked dengue virus envelope glycoprotein dimers reduce exposure of the immunodominant fusion loop epitope. Authors: Rouvinski, A. / Dejnirattisai, W. / Guardado-Calvo, P. / Vaney, M.C. / Sharma, A. / Duquerroy, S. / Supasa, P. / Wongwiwat, W. / Haouz, A. / Barba-Spaeth, G. / Mongkolsapaya, J. / Rey, F.A. / Screaton, G.R. #1: 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.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / Dejnirattisai, W. / Wongwiwat, W. / Haouz, A. / Girard-Blanc, C. ...Authors: Rouvinski, A. / Guardado-Calvo, P. / Barba-Spaeth, G. / Duquerroy, S. / Vaney, M.C. / Kikuti, C.M. / Navarro Sanchez, M.E. / 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n09.cif.gz | 657.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n09.ent.gz | 548.4 KB | Display | PDB format |
PDBx/mmJSON format | 5n09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n09_validation.pdf.gz | 567.9 KB | Display | wwPDB validaton report |
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Full document | 5n09_full_validation.pdf.gz | 603.9 KB | Display | |
Data in XML | 5n09_validation.xml.gz | 59.7 KB | Display | |
Data in CIF | 5n09_validation.cif.gz | 80.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/5n09 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/5n09 | HTTPS FTP |
-Related structure data
Related structure data | 5n0aC 4utbS S: Starting model for refinement C: citing same article (ref.) |
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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 , 2 types, 4 molecules HILM
#2: Antibody | Mass: 30355.521 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FAB FRAGMENT HEAVY CHAIN / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) #3: Antibody | Mass: 23107.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: FAB FRAGMENT LIGHT CHAIN / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) |
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-Protein / Non-polymers , 2 types, 4 molecules AB
#1: Protein | Mass: 47467.156 Da / Num. of mol.: 2 / Mutation: L107C A313C Source method: isolated from a genetically manipulated source Details: The specific strain used in this work, FGA02, (without engineered mutations) has been sequenced and deposited previously and corresponds to GenBank: KM087965.1 Source: (gene. exp.) Dengue virus 2 / Variant: FGA-02 / Plasmid: PMT/BIP/V5-HIS / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: C3VXD1, UniProt: A0A0B4SHY9*PLUS #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 3 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / | |
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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: 2.7 Å3/Da / Density % sol: 54.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100mM Tris pH 8.5 20.7% PEG 4K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 3.9→40 Å / Num. obs: 19970 / % possible obs: 96.9 % / Redundancy: 5.1 % / CC1/2: 0.891 / Rmerge(I) obs: 0.686 / Rpim(I) all: 0.354 / Net I/σ(I): 2.4 |
Reflection shell | Resolution: 3.9→4.27 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.965 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 23344 / CC1/2: 0.508 / Rpim(I) all: 1.044 / % possible all: 98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UTB Resolution: 3.9→39.991 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.87
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→39.991 Å
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Refine LS restraints |
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LS refinement shell |
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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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