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- EMDB-27077: Cryo-EM structure of TTMV-LY1 anellovirus virus-like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-27077
TitleCryo-EM structure of TTMV-LY1 anellovirus virus-like particle
Map data
Sample
  • Virus: TTV-like mini virus
    • Protein or peptide: Capsid protein
Keywordsanellovirus / VIRUS LIKE PARTICLE
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) / TTV-like mini virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsLiou SH / Delagrave S / Swanson K
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27077.png

Downloads & links

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Map

FileDownload / File: emd_27077.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.92 Å/pix.
x 440 pix.
= 406.12 Å		0.92 Å/pix.
x 440 pix.
= 406.12 Å		0.92 Å/pix.
x 440 pix.
= 406.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.923 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.87
Minimum - Maximum-10.423503999999999 - 14.535937000000001
Average (Standard dev.)0.000000000002534 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 406.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : TTV-like mini virus

EntireName: TTV-like mini virus
Components
  • Virus: TTV-like mini virus
    • Protein or peptide: Capsid protein

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Supramolecule #1: TTV-like mini virus

SupramoleculeName: TTV-like mini virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 93678 / Sci species name: TTV-like mini virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Details: TTV-like mini virus isolate TTMV_LY1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Anelloviridae (virus)
Molecular weightTheoretical: 79.869227 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPWWYRRRSY NPWRRRNWFR RPRKTIYRRY RRRRRWVRRK PFYKRKIKRL NIVEWQPKSI RKCRIKGMLC LFQTTEDRLS YNFDMYEES IIPEKLPGGG GFSIKNISLY ALYQEHIHAH NIFTHTNTDR PLARYTGCSL KFYQSKDIDY VVTYSTSLPL R SSMGMYNS ...String:
MPWWYRRRSY NPWRRRNWFR RPRKTIYRRY RRRRRWVRRK PFYKRKIKRL NIVEWQPKSI RKCRIKGMLC LFQTTEDRLS YNFDMYEES IIPEKLPGGG GFSIKNISLY ALYQEHIHAH NIFTHTNTDR PLARYTGCSL KFYQSKDIDY VVTYSTSLPL R SSMGMYNS MQPSIHLMQQ NKLIVPSKQT QKRRKPYIKK HISPPTQMKS QWYFQHNIAN IPLLMIRTTA LTLDNYYIGS RQ LSTNVTI HTLNTTYIQN RDWGDRNKTY YCQTLGTQRY FLYGTHSTAQ NINDIKLQEL IPLTNTQDYV QGFDWTEKDK HNI TTYKEF LTKGAGNPFH AEWITAQNPV IHTANSPTQI EQIYTASTTT FQNKKLTDLP TPGYIFITPT VSLRYNPYKD LAER NKCYF VRSKINAHGW DPEQHQELIN SDLPQWLLLF GYPDYIKRTQ NFALVDTNYI LVDHCPYTNP EKTPFIPLST SFIEG RSPY SPSDTHEPDE EDQNRWYPCY QYQQESINSI CLSGPGTPKI PKGITAEAKV KYSFNFKWGG DLPPMSTITN PTDQPT YVV PNNFNETTSL QNPTTRPEHF LYSFDERRGQ LTEKATKRLL KDWETKETSL LSTEYRFAEP TQTQAPQEDP SSEEEEE SN LFERLLRQRT KQLQLKRRII QTLKDLQKLE

UniProtKB: Capsid 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 19.59 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 6271
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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