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- EMDB-8984: Icosahedral cryo-EM structure of mature Kunjin virus -

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Basic information

Database: EMDB / ID: 8984
TitleIcosahedral cryo-EM structure of mature Kunjin virus
Map dataIcosahedral reconstruction of mature Kunjin virus.
SampleKunjin virus (STRAIN MRM61C):
virus / Glycoprotein shell / Nucleocapsid core
SourceKunjin virus (STRAIN MRM61C)
Methodsingle particle reconstruction / cryo EM / 6.4 Å resolution
AuthorsTherkelsen MD / Klose T / Vago F / Jiang W / Rossmann MG / Kuhn RJ
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Flaviviruses have imperfect icosahedral symmetry.
Authors: Matthew D Therkelsen / Thomas Klose / Frank Vago / Wen Jiang / Michael G Rossmann / Richard J Kuhn
DateDeposition: Jul 21, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_8984.map.gz (map file in CCP4 format, 131073 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
320 pix
3.24 Å/pix.
= 1036.8 Å
320 pix
3.24 Å/pix.
= 1036.8 Å
320 pix
3.24 Å/pix.
= 1036.8 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.24 Å
Contour Level:0.015 (by author), 0.015 (movie #1):
Minimum - Maximum-0.024628378 - 0.092042305
Average (Standard dev.)-0.000005962573 (0.005593918)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1036.8 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.243.243.24
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z1036.8001036.8001036.800
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0250.092-0.000

Supplemental data

Sample components

Entire Kunjin virus (STRAIN MRM61C)

EntireName: Kunjin virus (STRAIN MRM61C) / Details: Mature Kunjin virus purified from Vero cells. / Number of components: 3

Component #1: virus, Kunjin virus (STRAIN MRM61C)

VirusName: Kunjin virus (STRAIN MRM61C) / Class: VIRION / Details: Mature Kunjin virus purified from Vero cells. / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Kunjin virus (STRAIN MRM61C)
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: capsid shell / Diameter: 500.0 Å / T number(triangulation number): 3

Component #2: cellular-component, Glycoprotein shell

Cellular-componentName: Glycoprotein shell / Recombinant expression: No
SourceSpecies: Kunjin virus (STRAIN MRM61C)

Component #3: cellular-component, Nucleocapsid core

Cellular-componentName: Nucleocapsid core / Recombinant expression: No
SourceSpecies: Kunjin virus (STRAIN MRM61C)

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 85 % / Details: Blot for 8 seconds before plunging..

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: K ( 80.0 - 80.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 369

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 9206
3D reconstructionSoftware: RELION / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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