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- PDB-8cyg: Cryo-EM structure of TTMV-LY1 anellovirus virus-like particle -

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Basic information

Entry
Database: PDB / ID: 8cyg
TitleCryo-EM structure of TTMV-LY1 anellovirus virus-like particle
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / anellovirus
Function / homologyTT viral protein of unknown function / TT viral orf 1 / T=1 icosahedral viral capsid / Capsid protein
Function and homology information
Biological speciesAnelloviridae (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsLiou, S.H. / Delagrave, S. / Swanson, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2024
Title: Structure of anellovirus-like particles reveal a mechanism for immune evasion.
Authors: Shu-Hao Liou / Rajendra Boggavarapu / Noah R Cohen / Yue Zhang / Ishwari Sharma / Lynn Zeheb / Nidhi Mukund Acharekar / Hillary D Rodgers / Saadman Islam / Jared Pitts / Cesar Arze / Harish ...Authors: Shu-Hao Liou / Rajendra Boggavarapu / Noah R Cohen / Yue Zhang / Ishwari Sharma / Lynn Zeheb / Nidhi Mukund Acharekar / Hillary D Rodgers / Saadman Islam / Jared Pitts / Cesar Arze / Harish Swaminathan / Nathan Yozwiak / Tuyen Ong / Roger J Hajjar / Yong Chang / Kurt A Swanson / Simon Delagrave /
Abstract: Anelloviruses are nonpathogenic viruses that comprise a major portion of the human virome. Despite being ubiquitous in the human population, anelloviruses (ANVs) remain poorly understood. Basic ...Anelloviruses are nonpathogenic viruses that comprise a major portion of the human virome. Despite being ubiquitous in the human population, anelloviruses (ANVs) remain poorly understood. Basic features of the virus, such as the identity of its capsid protein and the structure of the viral particle, have been unclear until now. Here, we use cryogenic electron microscopy to describe the first structure of an ANV-like particle. The particle, formed by 60 jelly roll domain-containing ANV capsid proteins, forms an icosahedral particle core from which spike domains extend to form a salient part of the particle surface. The spike domains come together around the 5-fold symmetry axis to form crown-like features. The base of the spike domain, the P1 subdomain, shares some sequence conservation between ANV strains while a hypervariable region, forming the P2 subdomain, is at the spike domain apex. We propose that this structure renders the particle less susceptible to antibody neutralization by hiding vulnerable conserved domains while exposing highly diverse epitopes as immunological decoys, thereby contributing to the immune evasion properties of anelloviruses. These results shed light on the structure of anelloviruses and provide a framework to understand their interactions with the immune system.
History
DepositionMay 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Capsid protein
a: Capsid protein
b: Capsid protein
c: Capsid protein
d: Capsid protein
3: Capsid protein
4: Capsid protein
5: Capsid protein
6: Capsid protein
7: Capsid protein
I: Capsid protein
J: Capsid protein
K: Capsid protein
L: Capsid protein
M: Capsid protein
e: Capsid protein
f: Capsid protein
g: Capsid protein
h: Capsid protein
i: Capsid protein
j: Capsid protein
k: Capsid protein
l: Capsid protein
m: Capsid protein
n: Capsid protein
o: Capsid protein
p: Capsid protein
q: Capsid protein
r: Capsid protein
s: Capsid protein
t: Capsid protein
u: Capsid protein
v: Capsid protein
w: Capsid protein
x: Capsid protein
y: Capsid protein
1: Capsid protein
2: Capsid protein
O: Capsid protein
z: Capsid protein
A: Capsid protein
B: Capsid protein
D: Capsid protein
E: Capsid protein
F: Capsid protein
G: Capsid protein
H: Capsid protein
N: Capsid protein
P: Capsid protein
Q: Capsid protein
R: Capsid protein
T: Capsid protein
U: Capsid protein
V: Capsid protein
W: Capsid protein
X: Capsid protein
Y: Capsid protein
Z: Capsid protein
C: Capsid protein
S: Capsid protein


Theoretical massNumber of molelcules
Total (without water)4,792,15460
Polymers4,792,15460
Non-polymers00
Water00
1


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

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Components

#1: Protein ...
Capsid protein


Mass: 79869.227 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Details: TTV-like mini virus isolate TTMV_LY1 / Source: (gene. exp.) Anelloviridae (virus) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: M4NKL5

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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: TTV-like mini virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: TTV-like mini virus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 19.59 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: Gctf / Category: CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6271 / Symmetry type: POINT

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