+Open data
-Basic information
Entry | Database: PDB / ID: 3j35 | ||||||
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Title | Cryo-EM reconstruction of Dengue virus at 37 C | ||||||
Components | envelope protein | ||||||
Keywords | VIRUS / bumpy structure / conformational change / temperature dependent | ||||||
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 / clathrin-dependent endocytosis of virus by host cell ...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 / 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 / induction by virus of host autophagy / serine-type endopeptidase activity / 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 / endoplasmic reticulum membrane / virion attachment to host cell / structural molecule activity / virion membrane / 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: 35 Å | ||||||
Authors | Zhang, X.Z. / Sheng, J. / Plevka, P. / Kuhn, R.J. / Diamond, M.S. / Rossmann, M.G. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Dengue structure differs at the temperatures of its human and mosquito hosts. Authors: Xinzheng Zhang / Ju Sheng / Pavel Plevka / Richard J Kuhn / Michael S Diamond / Michael G Rossmann / Abstract: We report on a conformational transition of dengue virus when changing the temperature from that present in its mosquito vectors to that of its human host. Using cryoelectron microscopy, we show that ...We report on a conformational transition of dengue virus when changing the temperature from that present in its mosquito vectors to that of its human host. Using cryoelectron microscopy, we show that although the virus has a smooth surface, a diameter of ∼500 Å, and little exposed membrane at room temperature, the virions have a bumpy appearance with a diameter of ∼550 Å and some exposed membrane at 37 °C. The bumpy structure at 37 °C was found to be similar to the previously predicted structure of an intermediate between the smooth mature and fusogenic forms. As humans have a body temperature of 37 °C, the bumpy form of the virus would be the form present in humans. Thus, optimal dengue virus vaccines should induce antibodies that preferentially recognize epitopes exposed on the bumpy form of the virus. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j35.cif.gz | 52.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3j35.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 3j35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j35_validation.pdf.gz | 706.4 KB | Display | wwPDB validaton report |
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Full document | 3j35_full_validation.pdf.gz | 706 KB | Display | |
Data in XML | 3j35_validation.xml.gz | 20 KB | Display | |
Data in CIF | 3j35_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/3j35 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/3j35 | HTTPS FTP |
-Related structure data
Related structure data | 5587MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 43790.305 Da / Num. of mol.: 3 / Fragment: UNP residues 281-675 / Source method: isolated from a natural source / Source: (natural) Dengue virus 2 / References: UniProt: D0EPS0, UniProt: E7FLK7*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dengue virus at 37 C / Type: VIRUS |
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Details of virus | Empty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | Name: NTE / pH: 7.3 / Details: NTE |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temp: 100 K Details: Plunged into liquid ethane using a homemade plunger. |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG / Date: Jan 1, 2012 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 38000 X / Calibrated magnification: 39190 X / Cs: 2 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 168 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: Film | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Resolution: 35 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 515 / Actual pixel size: 3.3 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--rigid body | ||||||||||||
Atomic model building | 3D fitting-ID: 1 / Accession code: 3C6R / Initial refinement model-ID: 1 / PDB-ID: 3C6R / Source name: PDB / Type: experimental model
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Refinement step | Cycle: LAST
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