[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

TitleGermline-targeting HIV immunogen induces cross-neutralizing antibodies in outbred macaques.
Journal, issue, pagesImmunity, Vol. 59, Issue 4, Page 1140-1160.e11, Year 2026
Publish dateApr 14, 2026
AuthorsNitesh Mishra / Bo Liang / Ryan S Roark / Amrit Raj Ghosh / Sean Callaghan / Wen-Hsin Lee / Xuduo Li / Anh L Vo / Gabriel Avillion / Rohan Roy Chowdhury / Rumi Habib / Frederic Bibollet-Ruche / Gabriella Giese / Prabhgun Oberoi / Khaled Amereh / Anjali Somanathan / Yuxin Zhu / Yuexiu Zhang / Muzaffer Kassab / Lifei Tjio / Sharaf Andrabi / Raphael A Reyes / Joel D Allen / Nicole E James / Kipchoge N Randall / Lara van der Maas / Elana Ben-Akiva / Kasia Kacmarek-Michaels / Samantha Plante / Christian L Martella / Ashwin N Skelly / Ajay Singh / Jonathan Hurtado / Katharina Dueker / Tazio Capozzola / Rebecca Nedellec / Gabriel Ozorowski / Mark G Lewis / Samantha Falcone / Andrea Carfi / Sunny Himansu / Lawrence Shapiro / Max Crispin / Beatrice H Hahn / Bryan Briney / Darrell J Irvine / Dennis R Burton / Andrew B Ward / Facundo D Batista / Peter D Kwong / George M Shaw / Raiees Andrabi /
PubMed AbstractGermline targeting (GT) is a promising strategy to activate rare broadly neutralizing antibody (bnAb)-producing B cells against HIV, but induction of such responses in outbred animals has not been ...Germline targeting (GT) is a promising strategy to activate rare broadly neutralizing antibody (bnAb)-producing B cells against HIV, but induction of such responses in outbred animals has not been achieved. Using antibody-guided structure-based design, we engineered a GT HIV trimer immunogen, Q23-APEX-GT2, which primes diverse V2-apex bnAb precursors. Q23-APEX-GT2 efficiently activated rare V2-apex-specific B cells in humanized knockin mice and consistently elicited immunofocused antibody responses in outbred rhesus macaques, priming multiple long heavy-chain complementarity-determining region 3 (CDRH3)-loop bnAb-B cell lineages. Monoclonal antibodies isolated from immunized macaques showed broad heterologous HIV trimer recognition and modest cross-neutralization of diverse tier-2 viruses. Cryoelectron microscopy (cryo-EM) structural studies confirmed precise epitope targeting and revealed CDRH3-mediated binding modes that mirrored those of human V2-apex bnAbs. Together, these findings establish proof of principle for priming and early maturation of authentic V2-apex bnAb precursors in outbred macaques and highlight the promise of V2-apex-targeted HIV vaccines.
External linksImmunity / PubMed:41985438
MethodsEM (single particle)
Resolution2.9 - 25.0 Å
Structure data

EMDB-49511: CH35 V1V2V3 and gp41-base macaque polyclonal Fabs in complex with Q23-APEX-GT2 trimer
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-49512: CH35 gp41-FP macaque polyclonal Fab in complex with Q23-APEX-GT2 trimer
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-49513: CH70 gp41-GH macaque polyclonal Fab in complex with Q23-APEX-GT2 trimer
Method: EM (single particle) / Resolution: 25.0 Å

49865

9nvv

EMDB-49865, PDB-9nvv:
Cryo-EM structure of V2 apex germline-targeting HIV Env trimer Q23-APEX-GT2
Method: EM (single particle) / Resolution: 2.9 Å

49866

9nvw

EMDB-49866, PDB-9nvw:
Cryo-EM structure of rhesus antibody CH35-Apex1.08 in complex with HIV Env trimer Q23-APEX-GT2
Method: EM (single particle) / Resolution: 3.3 Å

49867

9nvx

EMDB-49867, PDB-9nvx:
Cryo-EM structure of rhesus antibody CI91-Apex1.01 in complex with HIV Env trimer Q23-APEX-GT2
Method: EM (single particle) / Resolution: 3.0 Å

49868

9nvy

EMDB-49868, PDB-9nvy:
Cryo-EM structure of rhesus antibody CH70-Apex2.01 in complex with HIV Env trimer Q23-APEX-GT2
Method: EM (single particle) / Resolution: 3.8 Å

49869

9nvz

EMDB-49869, PDB-9nvz:
Cryo-EM structure of rhesus antibody CH70-Apex1.01 in complex with HIV Env trimer Q23-APEX-GT2
Method: EM (single particle) / Resolution: 3.0 Å

49870

9nw0

EMDB-49870, PDB-9nw0:
Cryo-EM structure of rhesus antibody CH42-Apex1.01 in complex with HIV Env trimer Q23-APEX-GT2
Method: EM (single particle) / Resolution: 2.9 Å

49871

9nw1

EMDB-49871, PDB-9nw1:
Cryo-EM structure of rhesus antibody CH42-Apex2.01 in complex with HIV Env trimer Q23-APEX-GT2
Method: EM (single particle) / Resolution: 3.1 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-MAN:
alpha-D-mannopyranose

Source
  • macaca mulatta (Rhesus monkey)
  • human immunodeficiency virus type 1
  • human immunodeficiency virus 1
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / VIRAL PROTEIN / GERMLINE-TARGETING / IMMUNOGEN / VIRAL PROTEIN-IMMUNE SYSTEM complex / immune complex / neutralization / V2 apex / VIRAL PROTEIN/IMMUE SYSTEM / VIRAL PROTEIN-IMMUE SYSTEM complex

+
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