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

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Basic information

Entry
Database: EMDB / ID: EMD-3822
TitleStructure of the full-length African cichlid nackednavirus icosahedral capsid
Map dataStructure of the full-length African cichlid nackednavirus capsid.
Sample
  • Virus: Retro-transcribing viruses
Biological speciesRetro-transcribing viruses
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 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: 0.019
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.019
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3822.png

Downloads & links

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Map

FileDownload / File: emd_3822.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the full-length African cichlid nackednavirus capsid.
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.019 / Movie #1: 0.019
Minimum - Maximum-0.012712868 - 0.045723062
Average (Standard dev.)0.00028229013 (±0.003771977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 552.96 Å
α=β=γ: 90.0 °

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
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-0.0130.0460.000

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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: Full-length capsid (aa1-174) / 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 TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling 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: 1548 / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 53431
Details: manual picking of a few hundred for template production, then automated
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: NONE
Details: A spherical density with diameter of 40 nm was provided as an initial model
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.2)
Final 3D classificationNumber classes: 20 / Software - Name: RELION (ver. 1.2)
Details: 2D classification was performed using first IMAGIC and then RELION 1.2 to select regular, intact particles and remove disrupted ones.
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.2)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.2) / Number images used: 2547

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