[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

TitleMultifunctional antibody responses from a primate outbreak inform vaccine design.
Journal, issue, pagesSci Transl Med, Vol. 18, Issue 865, Page eaef7084, Year 2026
Publish dateSep 2, 2026
AuthorsRobert M Gallant / Paul Savarino / Sophia Pulido / Morgan S A Gilman / Ti Lu / Jennifer Hayes / Nicholas L Xerri / Torrey Williams / Mark A Ochoa / Zackary Dietz / Eric Peterson / Timothy Scott / Faye Hartmann / Stephen G Baker / Robert W Kaminski / Devin Sok / Andrew C Kruse / Wendy Picking / Saverio V Capuano / Hayden R Schmidt /
PubMed AbstractThere is currently no approved vaccine for spp., a leading cause of diarrhea with increasing rates of antimicrobial resistance. vaccine development is complicated in part by an incomplete ...There is currently no approved vaccine for spp., a leading cause of diarrhea with increasing rates of antimicrobial resistance. vaccine development is complicated in part by an incomplete understanding of the structural and molecular determinants of immunity. To address this, we isolated monoclonal antibodies against candidate vaccine antigens using samples from a outbreak in a nonhuman primate (NHP) research facility. We found that antibodies targeting the O-antigen can undergo substantial affinity maturation (>10%) to acquire broad cross-reactivity across serotypes. We also found that the virulence-associated type III secretion system (T3SS) proteins IpaD and IpaB elicit moderate T cell and robust antibody responses. T3SS antibodies could either inhibit or enhance bacterial virulence in vitro and differed in vivo depending on their epitope specificity. Collectively, these findings provide insights into protective and deleterious immune responses against that directly inform vaccine immunogen design.
External linksSci Transl Med / PubMed:42685149
MethodsEM (single particle)
Resolution3.3 - 3.4 Å
Structure data

EMDB-74629, PDB-9zrs:
Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking Fab D02-F2 and hemolysis enhancing Fab D02-E4
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-74630, PDB-9zrt:
Shigella flexneri type III secretion system (T3SS) protein IpaD bound to hemolysis blocking antibody fragment D13r-34
Method: EM (single particle) / Resolution: 3.3 Å

Source
  • shigella flexneri (bacteria)
  • macaca mulatta (Rhesus monkey)
KeywordsPROTEIN TRANSPORT / T3SS / epitope / vaccine antigen / SipD homolog

+
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