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

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Basic information

Entry
Database: PDB / ID: 8c0o
TitleAfrican cichlid nackednavirus capsid at pH 5.5
ComponentsC protein
KeywordsVIRAL PROTEIN / T=3 / Capsid protein
Function / homologyC protein
Function and homology information
Biological speciesAfrican cichlid nackednavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsPfister, S. / Rabl, J. / Boehringer, D. / Meier, B.H.
Funding supportEuropean Union, Switzerland, 3items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: C protein
AC: C protein
BA: C protein
BB: C protein
BC: C protein
CA: C protein
CB: C protein
CC: C protein
DA: C protein
DB: C protein
DC: C protein
EA: C protein
EB: C protein
EC: C protein
FA: C protein
FB: C protein
FC: C protein
GA: C protein
GB: C protein
GC: C protein
HA: C protein
HB: C protein
HC: C protein
IA: C protein
IB: C protein
IC: C protein
JA: C protein
1B: C protein
JB: C protein
JC: C protein
KA: C protein
KB: C protein
KC: C protein
LA: C protein
LB: C protein
LC: C protein
MA: C protein
MB: C protein
MC: C protein
NA: C protein
NB: C protein
NC: C protein
OA: C protein
OB: C protein
OC: C protein
PA: C protein
PB: C protein
PC: C protein
QA: C protein
QB: C protein
QC: C protein
RA: C protein
RB: C protein
RC: C protein
1C: C protein
SA: C protein
SB: C protein
SC: C protein
TA: C protein
TB: C protein
TC: C protein
UA: C protein
UB: C protein
UC: C protein
VA: C protein
VB: C protein
VC: C protein
WA: C protein
WB: C protein
WC: C protein
XA: C protein
XB: C protein
XC: C protein
YA: C protein
YB: C protein
YC: C protein
ZA: C protein
ZB: C protein
ZC: C protein
aA: C protein
aB: C protein
2A: C protein
aC: C protein
bA: C protein
bB: C protein
bC: C protein
cA: C protein
cB: C protein
cC: C protein
dA: C protein
dB: C protein
dC: C protein
eA: C protein
eB: C protein
eC: C protein
fA: C protein
fB: C protein
fC: C protein
gA: C protein
gB: C protein
gC: C protein
hA: C protein
hB: C protein
hC: C protein
iA: C protein
iB: C protein
iC: C protein
jA: C protein
2B: C protein
jB: C protein
jC: C protein
kA: C protein
kB: C protein
kC: C protein
lA: C protein
lB: C protein
lC: C protein
mA: C protein
mB: C protein
mC: C protein
nA: C protein
nB: C protein
nC: C protein
oA: C protein
oB: C protein
oC: C protein
pA: C protein
pB: C protein
pC: C protein
qA: C protein
qB: C protein
qC: C protein
rA: C protein
rB: C protein
rC: C protein
2C: C protein
sA: C protein
sB: C protein
sC: C protein
tA: C protein
tB: C protein
tC: C protein
uA: C protein
uB: C protein
uC: C protein
vA: C protein
vB: C protein
vC: C protein
wA: C protein
wB: C protein
wC: C protein
xA: C protein
xB: C protein
xC: C protein
yA: C protein
yB: C protein
yC: C protein
zA: C protein
zB: C protein
zC: C protein
3A: C protein
3B: C protein
3C: C protein
4A: C protein
4B: C protein
4C: C protein
5A: C protein
5B: C protein
5C: C protein
6A: C protein
6B: C protein
6C: C protein
7A: C protein
7B: C protein
7C: C protein
8A: C protein
8B: C protein
8C: C protein
AA: C protein
AB: C protein


Theoretical massNumber of molelcules
Total (without water)3,573,222180
Polymers3,573,222180
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
C protein


Mass: 19851.234 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African cichlid nackednavirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3S9H6T3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: African cichlid nackednavirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 3.57 MDa / Experimental value: NO
Source (natural)Organism: African cichlid nackednavirus
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pRSF_T7
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Ophthalmotilapia ventralis
Virus shellName: capsid / Diameter: 230 nm / Triangulation number (T number): 3
Buffer solutionpH: 5.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium acetateacetate1
250 mMSodium chlorideNaClSodium chloride1
35 mMEDTAEthylenediaminetetraacetic acidEDTAEthylenediaminetetraacetic acid1
45 mMDTTDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The protein concentration is approx. 0.1-0.5 mg/mL
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 166000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 5362
EM imaging opticsEnergyfilter slit width: 20 eV
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameVersionCategory
1crYOLO1.7.6particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7Coot0.8.9model fitting
9PHENIX1.17.1-3660model refinement
10ISOLDE1.0b4.dev0model refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 215225
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77129 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Details: One 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.

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