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

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Basic information

Entry
Database: EMDB / ID: EMD-3823
TitleStructure of the truncated African cichlid nackednavirus icosahedral capsid
Map dataStructure of the truncated African cichlid nackednavirus capsid
Sample
  • Virus: Retro-transcribing viruses
Biological speciesRetro-transcribing viruses
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
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.
History
DepositionJul 21, 2017-
Header (metadata) releaseAug 2, 2017-
Map releaseSep 13, 2017-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

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

emd_3823.png

Downloads & links

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Map

FileDownload / File: emd_3823.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the truncated African cichlid nackednavirus capsid
Voxel sizeX=Y=Z: 1.18 Å
Density
Contour LevelBy AUTHOR: 0.042 / Movie #1: 0.042
Minimum - Maximum-0.03903188 - 0.10546035
Average (Standard dev.)0.0007083466 (±0.0072973506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 604.16 Å
α=β=γ: 90.0 °

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
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
Components
  • Virus: Retro-transcribing viruses

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Supramolecule #1: Retro-transcribing viruses

SupramoleculeName: Retro-transcribing viruses / type: virus / ID: 1 / Parent: 0
Details: truncated capsid variant (aa 1-146) lacking the C-terminal nucleic acid binding domain.
NCBI-ID: 35268 / Sci species name: Retro-transcribing viruses / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Ophthalmotilapia ventralis (fish)
Host systemOrganism: Escherichia coli (E. coli)
Virus shellShell ID: 1 / Name: capsid / Diameter: 320.0 Å / T number (triangulation number): 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
GridModel: Protochips C-Flat / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: 20 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 1018 / Average electron dose: 35.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 781 / Details: manual picking
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER
Details: The structure of full-length ACNDV low-pass filtered at 100 angstrom was used as initial reference
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 260 / Software - Name: RELION (ver. 1.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.3)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 360

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