[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleRational Design of Multiclade Coronavirus Spike Immunodominant Domain Nanoparticles to Elicit Broad Antibody Responses.
Journal, issue, pagesRes Sq, Year 2025
Publish dateDec 10, 2025
AuthorsChristian K O Dzuvor / Sydney Moak / Lindsay R McManus / Abigail Thomas / Abigail E Dzordzorme / Taewoo Kim / Jeswin Joseph / Valerie Foley / Ingelise J Gordon / Laura Novik / LaSonji A Holman / Lesia K Dropulic / Ryan P McNamara / Kizzmekia S Corbett-Helaire /
PubMed AbstractFour seasonal endemic human coronaviruses (HCoVs), HCoV-HKU1, HCoV-OC43, HCoV-229E, and HCoV-NL63, are culprits of mild upper respiratory and periodic severe diseases in vulnerable populations. ...Four seasonal endemic human coronaviruses (HCoVs), HCoV-HKU1, HCoV-OC43, HCoV-229E, and HCoV-NL63, are culprits of mild upper respiratory and periodic severe diseases in vulnerable populations. Despite their prevalence, understanding HCoVs' antigenic and immune signatures remains elusive. SARS-CoV-2 has evolved as the fifth HCoV, requiring seasonal vaccination, and currently, no other HCoV vaccines are available. SARS-CoV-2 co-infection with HCoVs increases disease severity; thus, combined vaccination may provide increased protection against seasonal HCoVs overall. Here, we explored spike (S) receptor binding domain (RBD) vs. N-terminal domain (NTD) B-cell immunodominance in HCoV-positive convalescent donors and immunogenicity in mice. We found that while antibody and B-cell isotypes were relatively dominant to S NTD, mice immunized with S RBD elicited significantly higher binding and neutralizing antibody (nAb) responses. With that knowledge, we used computational methods to infer that HCoV S sequences evolve into two main clades and designed chimeric immunodominant domains (IDDs) from both clades for each HCoV. IDDs were scaffolded onto two-component nanoparticles (NPs) displaying each IDD separately (monovalent IDD NP); three ß-HCoV IDDs (Mosaic-3 IDD NP); or five HCoVs IDDs (Mosaic-5 IDD NP). Mice immunized with mosaic IDD NPs, but not soluble IDD antigens nor monovalent IDD NPs, elicited potent, broadly cross-reactive binding and neutralizing antibody (Ab) responses against SARS-CoV-2 variants, other HCoVs, and Sarbecoviruses. System serology revealed that all four IDD immunogens elicited distinct Ab subclasses and Fc-effector functions, with mosaic-5 IDD NPs eliciting the most Ab subclasses, distributions, and broader Fc-mediated immune mechanisms. Dissection of vaccine-immune sera revealed polyclonal Ab responses against multiple non-overlapping cross-reactive S epitopes. Due to elicitation of broad Ab responses with combinatory functionality, IDD NPs open new horizons for developing first-in-class supraseasonal HCoV vaccine candidates, with potential to decrease frequent SARS-CoV-2 sequence updates and protect against other HCoVs. Moreover, elicitation of Ab breadth that spans pandemic-threat Sarbecoviruses gives mosaic IDD NPs promise towards pandemic preparedness.
External linksRes Sq / PubMed:41472675 / PubMed Central
MethodsEM (single particle)
Resolution3.92 - 4.42 Å
Structure data

EMDB-73662: Structure of Mosaic -5 IDD NPs
Method: EM (single particle) / Resolution: 3.92 Å

EMDB-73675: Structure of SS-L2-I53-50NP
Method: EM (single particle) / Resolution: 4.42 Å

Source
  • Mammalian expression vector Flag-MCS-pcDNA3.1 (others)

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more