[English] 日本語
Yorodumi
- EMDB-43009: Cryo-EM structure of TTMV-LY1 anellovirus virus-like particle exp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43009
TitleCryo-EM structure of TTMV-LY1 anellovirus virus-like particle expressed in HEK293
Map data
Sample
  • Virus: TTV-like mini virus
    • Protein or peptide: Capsid protein
KeywordsAnello Virus: Virus Like Particle (VLP) / 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 speciesTTV-like mini virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsRajendra B / 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
DepositionDec 4, 2023-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateSep 4, 2024-
Current statusSep 4, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43009.png

Downloads & links

-
Map

FileDownload / File: emd_43009.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 500.4 Å		0.83 Å/pix.
x 600 pix.
= 500.4 Å		0.83 Å/pix.
x 600 pix.
= 500.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.834 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.113
Minimum - Maximum-0.19741425 - 0.37120187
Average (Standard dev.)0.0021794662 (±0.014869281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 500.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_43009_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_43009_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TTV-like mini virus

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

-
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

-
Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: TTV-like mini virus
Molecular weightTheoretical: 72.328844 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 KDWETK

UniProtKB: Capsid protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 1.4 sec. / Average electron dose: 50.53 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23193
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more