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
Deposition
Jan 23, 2013
-
Header (metadata) release
Feb 27, 2013
-
Map release
May 15, 2013
-
Update
May 15, 2013
-
Current status
May 15, 2013
Processing site: PDBe / Status: Released
-
Structure visualization
Movie
Surface view with section colored by density value
pH: 8 / Details: 10 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
Grid
Details: lacey carbon grid, layered with ultra thin carbon
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Method: 2.5 microlitres virus sample was added per grid and blotted with filter paper for 2.5 s before plunging
-
Electron microscopy
Microscope
FEI TITAN KRIOS
Temperature
Average: 100 K
Date
Nov 21, 2011
Image recording
Category: CCD / Film or detector model: GENERIC GATAN / Number real images: 302 / Average electron dose: 18.5 e/Å2
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi