[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

TitleStructural insights from vaccine candidates for EV-D68.
Journal, issue, pagesCommun Biol, Vol. 8, Issue 1, Page 860, Year 2025
Publish dateJun 4, 2025
AuthorsJiaxuan Cheng / Peter W Krug / Haotian Lei / Daniel L Moss / Zabrina C Lang / Abraham J Morton / Chen-Hsiang Shen / Sergei Pletnev / Rick K Huang / Theodore C Pierson / Tongqing Zhou / Tracy J Ruckwardt / Peter D Kwong /
PubMed AbstractEnterovirus D68 (EV-D68), a member of the Picornaviridae family, causes respiratory illness and can lead to acute flaccid myelitis in children. No specific treatment or vaccine is available. Here, we ...Enterovirus D68 (EV-D68), a member of the Picornaviridae family, causes respiratory illness and can lead to acute flaccid myelitis in children. No specific treatment or vaccine is available. Here, we determine cryo-EM structures of EV-D68 virus-like particles (VLPs), inactivated virus particles (InVPs), and altered virus particles (A-particles) from B3 and A2 subclades. The B3 VLP is a current vaccine candidate, which we show closely resembles its InVP counterpart, particularly at the 5-fold axis of symmetry, the target of potent neutralizing antibodies. Similar structural conservation was observed in the A2 subclade. Sequence variation between B3 and A2 mainly occurred in flexible loops displayed on the particle surface. A canyon-filling pocket factor was present in B3 InVP but absent in A2 InVP. A-particles were predominant in β-propiolactone-inactivated virus at longer but not shorter incubation. Overall, our findings highlight EV-D68 similarities and subclade-specific differences, offering structural insights that relate to vaccine development.
External linksCommun Biol / PubMed:40467847 / PubMed Central
MethodsEM (single particle)
Resolution2.42 - 3.96 Å
Structure data

45171

9c3j

EMDB-45171, PDB-9c3j:
Cryo-EM structure of EV-D68 B3 Virus-like particle
Method: EM (single particle) / Resolution: 2.42 Å

45179

9c4a

EMDB-45179, PDB-9c4a:
Cryo-EM Structure of EV-D68 Vaccine Candidate - A2 Subclade Virus-like Particle
Method: EM (single particle) / Resolution: 2.43 Å

45303

9c8f

EMDB-45303, PDB-9c8f:
Cryo-EM Structure of EV-D68 B3 A-Particle
Method: EM (single particle) / Resolution: 2.86 Å

45304

9c8g

EMDB-45304, PDB-9c8g:
Cryo-EM Structure of EV-D68 A2 Inactivated Virus Particle
Method: EM (single particle) / Resolution: 2.64 Å

45305

9c8h

EMDB-45305, PDB-9c8h:
Cryo-EM Structure of EV-D68 A2 A-Particle
Method: EM (single particle) / Resolution: 3.96 Å

45306

9c8i

EMDB-45306, PDB-9c8i:
Cryo-EM Structure of EV-D68 B3 Inactivated Virus Particle
Method: EM (single particle) / Resolution: 2.73 Å

Source
  • human enterovirus d68
KeywordsVIRUS LIKE PARTICLE / EV-D68 / B3 subclade / VLP / VIRUS-LIKE PARTICLE / A2 subclade

+
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