[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 basis for plasticity in receptor engagement by an encephalitic alphavirus.
Journal, issue, pagesCell, Vol. 188, Issue 11, Page 2943-2956.e24, Year 2025
Publish dateMay 29, 2025
AuthorsSaravanan Raju / Sathvik Palakurty / Alan Sariol / Ngan Wagoner / Lucas J Adams / Sean Hui / William B Klimstra / Daved H Fremont / Michael S Diamond /
PubMed AbstractThe structural basis for shifts in receptor usage remains poorly understood despite the implications for virus adaptation and emergence. Western equine encephalitis virus (WEEV) strains exhibit ...The structural basis for shifts in receptor usage remains poorly understood despite the implications for virus adaptation and emergence. Western equine encephalitis virus (WEEV) strains exhibit different patterns of engagement for two of their entry receptors: very-low-density lipoprotein receptor (VLDLR) and protocadherin 10 (PCDH10). Using structural and functional studies, we show that while all WEEV strains have a lipoprotein class A (LA) domain binding site near the E1 fusion loop, VLDLR engagement requires a second binding site in E2 that can vary with single nucleotide substitutions. We also resolve a structure of PCDH10 bound to WEEV, which reveals interactions near the E1 fusion loop with residues that also mediate LA domain binding. Evolutionary analysis enabled the generation of a PCDH10 decoy that protects in vivo against all WEEV strains tested. Our experiments demonstrate how viruses can engage multiple receptors using shared determinants, which likely impacts cellular tropism and virulence.
External linksCell / PubMed:40187344
MethodsEM (single particle)
Resolution3.06 - 4.51 Å
Structure data

47775

9e96

EMDB-47775, PDB-9e96:
WEEV CBA87 VLP in complex with human PCDH10-EC1
Method: EM (single particle) / Resolution: 4.05 Å

47821

9e9y

EMDB-47821, PDB-9e9y:
WEEV McMillan VLP in complex with VLDLR LA(1-2)
Method: EM (single particle) / Resolution: 3.96 Å

47822

9e9z

EMDB-47822, PDB-9e9z:
SINV-WEEV Fleming in complex with VLDLR LA(1-2)
Method: EM (single particle) / Resolution: 3.95 Å

47846

9eau

EMDB-47846, PDB-9eau:
RRV DKTA VLP in complex with VLDLR-LBD-Fc
Method: EM (single particle) / Resolution: 3.06 Å

EMDB-49104: WEEV McMillan VLP in complex with VLDLR-LBD-Fc ASU
Method: EM (single particle) / Resolution: 4.51 Å

EMDB-49105: WEEV McMillan VLP Apo
Method: EM (single particle) / Resolution: 3.69 Å

EMDB-49106: SINV-WEEV Fleming in complex with VLDLR-LBD-Fc ASU
Method: EM (single particle) / Resolution: 3.79 Å

Chemicals

ChemComp-CA:
Unknown entry

Source
  • western equine encephalitis virus
  • homo sapiens (human)
  • ross river virus (strain t48)
KeywordsVIRAL PROTEIN / Alphavirus Receptor / VIRUS

+
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