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- EMDB-3823: Structure of the truncated African cichlid nackednavirus icosahed... -

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Entry
Database: EMDB / ID: 3823
TitleStructure of the truncated African cichlid nackednavirus icosahedral capsid
Map dataStructure of the truncated African cichlid nackednavirus capsid
SampleRetro-transcribing viruses:
virus
SourceRetro-transcribing viruses
Methodsingle particle reconstruction / cryo EM / 9 Å resolution
AuthorsMattei S / Briggs JAG / Seitz S
CitationJournal: Cell Host Microbe / Year: 2017
Title: Deciphering the Origin and Evolution of Hepatitis B Viruses by Means of a Family of Non-enveloped Fish Viruses.
Authors: Chris Lauber / Stefan Seitz / Simone Mattei / Alexander Suh / Jürgen Beck / Jennifer Herstein / Jacob Börold / Walter Salzburger / Lars Kaderali / John A G Briggs / Ralf Bartenschlager
Abstract: Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome ...Hepatitis B viruses (HBVs), which are enveloped viruses with reverse-transcribed DNA genomes, constitute the family Hepadnaviridae. An outstanding feature of HBVs is their streamlined genome organization with extensive gene overlap. Remarkably, the ∼1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested within the ORF of the viral replicase P. Here, we report the discovery of a diversified family of fish viruses, designated nackednaviruses, which lack the envelope protein gene, but otherwise exhibit key characteristics of HBVs including genome replication via protein-primed reverse-transcription and utilization of structurally related capsids. Phylogenetic reconstruction indicates that these two virus families separated more than 400 million years ago before the rise of tetrapods. We show that HBVs are of ancient origin, descending from non-enveloped progenitors in fishes. Their envelope protein gene emerged de novo, leading to a major transition in viral lifestyle, followed by co-evolution with their hosts over geologic eras.
DateDeposition: Jul 21, 2017 / Header (metadata) release: Aug 2, 2017 / Map release: Sep 13, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3823.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.18 Å/pix.
= 604.16 Å
512 pix
1.18 Å/pix.
= 604.16 Å
512 pix
1.18 Å/pix.
= 604.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.18 Å
Density
Contour Level:0.042 (by author), 0.042 (movie #1):
Minimum - Maximum-0.03903188 - 0.10546035
Average (Standard dev.)0.0007083466 (0.0072973506)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin000
Limit511511511
Spacing512512512
CellA=B=C: 604.16 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.181.181.18
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z604.160604.160604.160
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0390.1050.001

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Supplemental data

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Sample components

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Entire Retro-transcribing viruses

EntireName: Retro-transcribing viruses
Details: truncated capsid variant (aa 1-146) lacking the C-terminal nucleic acid binding domain.
Number of components: 1

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Component #1: virus, Retro-transcribing viruses

VirusName: Retro-transcribing viruses / Class: VIRION
Details: truncated capsid variant (aa 1-146) lacking the C-terminal nucleic acid binding domain.
Empty: Yes / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Retro-transcribing viruses
Source (engineered)Expression System: Escherichia coli (E. coli)
Source (natural)Host Species: Ophthalmotilapia ventralis
Shell #1Name of element: capsid / Diameter: 320 Å / T number(triangulation number): 3

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.2
Support film20 mA
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 288 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 35 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4000 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1018 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 360
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 9 Å / Resolution method: FSC 0.143 CUT-OFF

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