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- EMDB-16371: African cichlid nackednavirus capsid at pH 5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-16371
TitleAfrican cichlid nackednavirus capsid at pH 5.5
Map dataRefined sharpened map of recombinant African Cichlid Nackednavirus capsid at pH 5.5
Sample
  • Virus: African cichlid nackednavirus
    • Protein or peptide: C protein
KeywordsT=3 / Capsid protein / VIRAL PROTEIN
Function / homologyC protein
Function and homology information
Biological speciesAfrican cichlid nackednavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPfister S / Rabl J / Boehringer D / Meier BH
Funding supportEuropean Union, Switzerland, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)741863European Union
Swiss National Science Foundation200020_159707 Switzerland
Swiss National Science Foundation200020_188711 Switzerland
CitationJournal: Nat Commun / Year: 2023
Title: Structural conservation of HBV-like capsid proteins over hundreds of millions of years despite the shift from non-enveloped to enveloped life-style.
Authors: Sara Pfister / Julius Rabl / Thomas Wiegand / Simone Mattei / Alexander A Malär / Lauriane Lecoq / Stefan Seitz / Ralf Bartenschlager / Anja Böckmann / Michael Nassal / Daniel Boehringer / Beat H Meier /
Abstract: The discovery of nackednaviruses provided new insight into the evolutionary history of the hepatitis B virus (HBV): The common ancestor of HBV and nackednaviruses was non-enveloped and while HBV ...The discovery of nackednaviruses provided new insight into the evolutionary history of the hepatitis B virus (HBV): The common ancestor of HBV and nackednaviruses was non-enveloped and while HBV acquired an envelope during evolution, nackednaviruses remained non-enveloped. We report the capsid structure of the African cichlid nackednavirus (ACNDV), determined by cryo-EM at 3.7 Å resolution. This enables direct comparison with the known capsid structures of HBV and duck HBV, prototypic representatives of the mammalian and avian lineages of the enveloped Hepadnaviridae, respectively. The sequence identity with HBV is 24% and both the ACNDV capsid protein fold and the capsid architecture are very similar to those of the Hepadnaviridae and HBV in particular. Acquisition of the hepadnaviral envelope was thus not accompanied by a major change in capsid structure. Dynamic residues at the spike tip are tentatively assigned by solid-state NMR, while the C-terminal domain is invisible due to dynamics. Solid-state NMR characterization of the capsid structure reveals few conformational differences between the quasi-equivalent subunits of the ACNDV capsid and an overall higher capsid structural disorder compared to HBV. Despite these differences, the capsids of ACNDV and HBV are structurally highly similar despite the 400 million years since their separation.
History
DepositionDec 19, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16371.png

Downloads & links

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Map

FileDownload / File: emd_16371.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined sharpened map of recombinant African Cichlid Nackednavirus capsid at pH 5.5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 432 pix.
= 362.88 Å		0.84 Å/pix.
x 432 pix.
= 362.88 Å		0.84 Å/pix.
x 432 pix.
= 362.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.032989837 - 0.050880015
Average (Standard dev.)0.00017846256 (±0.0030670583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 362.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of recombinant African Cichlid Nackednavirus capsid...

Fileemd_16371_half_map_1.map
AnnotationHalf map of recombinant African Cichlid Nackednavirus capsid at pH 5.5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of recombinant African Cichlid Nackednavirus capsid...

Fileemd_16371_half_map_2.map
AnnotationHalf map of recombinant African Cichlid Nackednavirus capsid at pH 5.5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : African cichlid nackednavirus

EntireName: African cichlid nackednavirus
Components
  • Virus: African cichlid nackednavirus
    • Protein or peptide: C protein

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Supramolecule #1: African cichlid nackednavirus

SupramoleculeName: African cichlid nackednavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2497433 / Sci species name: African cichlid nackednavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Ophthalmotilapia ventralis (fish)
Molecular weightTheoretical: 3.57 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 230.0 Å / T number (triangulation number): 3

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Macromolecule #1: C protein

MacromoleculeName: C protein / type: protein_or_peptide / ID: 1 / Number of copies: 180 / Enantiomer: LEVO
Source (natural)Organism: African cichlid nackednavirus
Molecular weightTheoretical: 19.851234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGTFIELVKN MKGYKELLLP MEMVPLPAVV LKHVKLILTS QKEHQPWMTE MALKADQCLI HKATLDLAGK ATSNEAKPLI EAMQQIILA MTRELWGQIQ RHHYGIVQVE HYVKQITLWQ DTPQAFRGDQ PKPPSFRSDG PTRGQGSFRP FFRGRGRGRG R GRGSQSPA RKGPLPK

UniProtKB: C protein

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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: 5.5
Component:
ConcentrationFormulaName
50.0 mMacetatesodium acetate
50.0 mMNaClSodium chloride
5.0 mMEDTAEDTA
5.0 mMDTTDTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThe protein concentration is approx. 0.1-0.5 mg/mL

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-40 / Number real images: 5362 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 166000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 215225
Startup modelType of model: OTHER
Details: Map of African cichlid nackednavirus capsid at pH 7.5
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 77129
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 10 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsOne protein chain was manually built in Coot. The chain was multiplied to give 180 chains, which were arranged as an icosahedral capsid. The capsid was refined with phenix and Isolde.
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8c0o:
African cichlid nackednavirus capsid at pH 5.5

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