[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

TitleImmunization with germ line-targeting SOSIP trimers elicits broadly neutralizing antibody precursors in infant macaques.
Journal, issue, pagesSci Immunol, Vol. 9, Issue 98, Page eadm7097, Year 2024
Publish dateAug 30, 2024
AuthorsAshley N Nelson / Xiaoying Shen / Sravani Vekatayogi / Shiyu Zhang / Gabriel Ozorowski / Maria Dennis / Leigh M Sewall / Emma Milligan / Dominique Davis / Kaitlyn A Cross / Yue Chen / Jelle van Schooten / Joshua Eudailey / John Isaac / Saad Memon / Carolyn Weinbaum / Hongmei Gao / Sherry Stanfield-Oakley / Alliyah Byrd / Suni Chutkan / Stella Berendam / Kenneth Cronin / Anila Yasmeen / S Alam / Celia C LaBranche / Kenneth Rogers / Lisa Shirreff / Albert Cupo / Ronald Derking / Francois Villinger / Per Johan Klasse / Guido Ferrari / Wilton B Williams / Michael G Hudgens / Andrew B Ward / David C Montefiori / Koen K A Van Rompay / Kevin Wiehe / John P Moore / Rogier W Sanders / Kristina De Paris / Sallie R Permar /
PubMed AbstractAdolescents are a growing population of people living with HIV. The period between weaning and sexual debut presents a low-risk window for HIV acquisition, making early childhood an ideal time for ...Adolescents are a growing population of people living with HIV. The period between weaning and sexual debut presents a low-risk window for HIV acquisition, making early childhood an ideal time for implementing an immunization regimen. Because the elicitation of broadly neutralizing antibodies (bnAbs) is critical for an effective HIV vaccine, our goal was to assess the ability of a bnAb B cell lineage-designed HIV envelope SOSIP (protein stabilized by a disulfide bond between gp120-gp41-named "SOS"-and an isoleucine-to-proline point mutation-named "IP"-at residue 559) to induce precursor CD4 binding site (CD4bs)-targeting bnAbs in early life. Infant rhesus macaques received either a BG505 SOSIP, based on the infant BG505 transmitted/founder virus, or the CD4bs germ line-targeting BG505 SOSIP GT1.1 ( = 5 per group). Although both strategies induced durable, high-magnitude plasma autologous virus neutralization responses, only GT1.1-immunized infants ( = 3 of 5) exhibited VRC01-like CD4bs bnAb precursor development. Thus, a multidose immunization regimen with bnAb lineage-designed SOSIPs shows promise for inducing early B cell responses with the potential to mature into protective HIV bnAbs before sexual debut.
External linksSci Immunol / PubMed:39213340
MethodsEM (single particle)
Resolution25.0 - 30.0 Å
Structure data

EMDB-41869: BG505.664 SOSIP in complex with polyclonal antibodies from NHP 8131 (gp120 glycan hole, gp41 glycan hole/fusion peptide and trimer base epitopes)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-41870: BG505.664 Env SOSIP in complex with polyclonal antibodies from NHP 8131 (gp120-gp120 interface epitope)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-41871: BG505.664 Env SOSIP in complex with polyclonal antibodies from NHP 8147 (C3/V5, V1/V2/V3 apex, gp41 glycan hole/fusion peptide and trimer base epitopes)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-41872: BG505.664 Env SOSIP in complex with polyclonal antibodies from NHP 8147 (gp120 glycan hole epitope)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-41972: GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP A12N030 (CD4bs, C3V5 and base epitopes)
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-41973: GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP A12N030 (gp41GH/FP and base epitopes)
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-41974: GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP DC8G (gp41GH/FP and gp120GH epitopes)
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-41975: GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP DC8G (gp120GH and base epitopes)
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-41976: GT1.1 SOSIP in complex with wk39 polyclonal antibodies from NHP DC8G (V1V2V3 and gp120GH epitopes)
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-41977: GT1.1 SOSIP-CC2 in complex with wk80 polyclonal antibodies from NHP 8229 (V1V2V3, C3V5, CD4bs, gp41GH/FP and base epitopes)
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-41978: GT1.1 SOSIP-CC2 in complex with wk80 polyclonal antibodies from NHP 8239 (gp120GH, gp41GH/FP, CD4bs, and base epitopes)
Method: EM (single particle) / Resolution: 25.0 Å

Source
  • Human immunodeficiency virus 1
  • Macaca (macaques)
  • Macaca mulatta (Rhesus monkey)

+
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