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- EMDB-3822: Structure of the full-length African cichlid nackednavirus icosah... -

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Basic information

Database: EMDB / ID: 3822
TitleStructure of the full-length African cichlid nackednavirus icosahedral capsid
SampleRetro-transcribing viruses
SourceRetro-transcribing viruses / virus
Map dataStructure of the full-length African cichlid nackednavirus capsid.
Methodsingle particle (icosahedral) reconstruction, at 8 Å resolution
AuthorsMattei S / Briggs JAG / Seitz S
CitationCell Host Microbe, 2017, 22, 387-399.e6

Cell Host Microbe, 2017, 22, 387-399.e6 Yorodumi Papers
Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses.
Chris Lauber / Stefan Seitz / Simone Mattei / Alexander Suh / Jürgen Beck / Jennifer Herstein / Jacob Börold / Walter Salzburger / Lars Kaderali / John A G Briggs / Ralf Bartenschlager

DateDeposition: Jul 21, 2017 / Header (metadata) release: Aug 2, 2017 / Map release: Sep 13, 2017 / Last update: Sep 27, 2017

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.019
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_3822.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.08 Å/pix.
= 552.96 Å
512 pix
1.08 Å/pix.
= 552.96 Å
512 pix
1.08 Å/pix.
= 552.96 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.08 Å
Contour Level:0.019 (by author), 0.019 (movie #1):
Minimum - Maximum-0.012712868 - 0.045723062
Average (Standard dev.)0.00028229013 (0.003771977)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 552.96 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z552.960552.960552.960
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-256-256-256
D min/max/mean-0.0130.0460.000

Supplemental data

Sample components

Entire Retro-transcribing viruses

EntireName: Retro-transcribing viruses / Details: Full-length capsid (aa1-174) / Number of components: 1

Component #1: virus, Retro-transcribing viruses

VirusName: Retro-transcribing viruses / Class: VIRION / Details: Full-length capsid (aa1-174) / Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Retro-transcribing viruses / virus
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (natural)Host Species: Ophthalmotilapia ventralis
Shell #1Name of element: capsid / Diameter: 320 Å / T number(triangulation number): 3

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.2
Support film20 mA
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 288 K / Humidity: 100 %

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: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4000 nm
CameraDetector: FEI FALCON II (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 1548 / Sampling size: 14 microns

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2547
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF

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