+Open data
-Basic information
Entry | Database: PDB / ID: 3zko | ||||||
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Title | The structure of ''breathing'' dengue virus. | ||||||
Components | ENVELOPE GLYCOPROTEIN | ||||||
Keywords | VIRUS / BREATHING STRUCTURE / DYNAMIC STRUCTURE | ||||||
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 / 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 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 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 13.7 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C | ||||||
Authors | Fibriansah, G. / Ng, T.S. / Kostyuchenko, V.A. / Lee, S. / Wang, J. / Lok, S.M. | ||||||
Citation | Journal: J Virol / Year: 2013 Title: Structural changes in dengue virus when exposed to a temperature of 37°C. Authors: Guntur Fibriansah / Thiam-Seng Ng / Victor A Kostyuchenko / Jaime Lee / Sumarlin Lee / Jiaqi Wang / Shee-Mei Lok / Abstract: Previous binding studies of antibodies that recognized a partially or fully hidden epitope suggest that insect cell-derived dengue virus undergoes structural changes at an elevated temperature. This ...Previous binding studies of antibodies that recognized a partially or fully hidden epitope suggest that insect cell-derived dengue virus undergoes structural changes at an elevated temperature. This was confirmed by our cryo-electron microscopy images of dengue virus incubated at 37°C, where viruses change their surface from smooth to rough. Here we present the cryo-electron microscopy structures of dengue virus at 37°C. Image analysis showed four classes of particles. The three-dimensional (3D) map of one of these classes, representing half of the imaged virus population, shows that the E protein shell has expanded and there is a hole at the 3-fold vertices. Fitting E protein structures into the map suggests that all of the interdimeric and some intradimeric E protein interactions are weakened. The accessibility of some previously found cryptic epitopes on this class of particles is discussed. | ||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 3zko.cif.gz | 54.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zko.ent.gz | 31.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zko.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zko_validation.pdf.gz | 746.4 KB | Display | wwPDB validaton report |
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Full document | 3zko_full_validation.pdf.gz | 746 KB | Display | |
Data in XML | 3zko_validation.xml.gz | 22 KB | Display | |
Data in CIF | 3zko_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/3zko ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zko | HTTPS FTP |
-Related structure data
Related structure data | 2296MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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