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- EMDB-2485: Near-atomic resolution cryo-EM structure of Dengue serotype 4 virus -

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Database: EMDB / ID: 2485
TitleNear-atomic resolution cryo-EM structure of Dengue serotype 4 virus
Keywordsflavivirus / virus / dengue virus serotype 4 / cryo-EM / dengue virus
SampleMature Dengue virus serotype 4
SourceDengue virus 4 / virus
Map dataMature dengue virus serotype 4 icosahedral reconstruction
Methodsingle particle (icosahedral) reconstruction, at 4.1 Å resolution
AuthorsKostyuchenko VA / Chew PL / Ng TS / Lok SM
CitationJ. Virol., 2014, 88, 477-482

J. Virol., 2014, 88, 477-482 Yorodumi Papers
Near-atomic resolution cryo-electron microscopic structure of dengue serotype 4 virus.
Victor A Kostyuchenko / Pau Ling Chew / Thiam-Seng Ng / Shee-Mei Lok

Validation ReportPDB-ID: 4cbf

SummaryFull reportAbout validation report
DateDeposition: Oct 14, 2013 / Header (metadata) release: Oct 23, 2013 / Map release: Nov 6, 2013 / Last update: Feb 17, 2016

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4cbf
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-4cbf
  • Imaged by Jmol
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3D viewer
Supplemental images

Downloads & links


Fileemd_2485.map.gz (map file in CCP4 format, 1024001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
640 pix
0.8 Å/pix.
= 512. Å
640 pix
0.8 Å/pix.
= 512. Å
640 pix
0.8 Å/pix.
= 512. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.8 Å
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-10.29256344 - 9.6550312
Average (Standard dev.)-0.11775072 (1.00091231)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 512 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.80.80.8
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000512.000
start NX/NY/NZ00-40
MAP C/R/S123
start NC/NR/NS-320-320-320
D min/max/mean-10.2939.655-0.118

Supplemental data

Sample components

Entire Mature Dengue virus serotype 4

EntireName: Mature Dengue virus serotype 4 / Number of components: 1

Component #1: virus, Dengue virus 4

VirusName: Dengue virus 4 / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: SEROTYPE
SpeciesSpecies: Dengue virus 4 / virus / Serotype: 4
Source (engineered)Expression System: Drosophila melanogaster / arthropod / /
Cell of expression system: c6/36
Source (natural)Host Species: Homo sapiens / human / / Host category: VERTEBRATES
Shell #1Name of element: glycoprotein shell / Diameter: 480 Å / T number(triangulation number): 1

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 12 mM Tris, 120 mM NaCl, 1 mM EDTA / pH: 8
Support filmthin carbon film
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 2 seconds before plunging

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Apr 14, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 125000 X (nominal), 129629 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 0.5 - 3.5 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 K
CameraDetector: FEI FALCON I (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 716 / Sampling size: 14 microns / Bit depth: 16

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 16602
Details: particles selected in EMAN2 boxer swarm mode, CTF estimated with ctffind3
3D reconstructionAlgorithm: Cross-common lines / Software: MPSA, EMAN, EMAN2 / CTF correction: each particle / Resolution: 4.1 Å / Resolution method: FSC 0.5

Atomic model buiding

Modeling #1Software: CHIMERA, Coot, CNS / Refinement protocol: flexible / Target criteria: real space correlation / Refinement space: REAL
Details: Initially fitted in Chimera, model rebuilt in Coot, refined in CNS
Input PDB model: 3j27
Chain ID: A, B, C, D, E, F
Output model

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