[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

TitleVaccination generates broadly cross-neutralizing antibodies to the HIV Env apex.
Journal, issue, pagesNature, Year 2026
Publish dateApr 29, 2026
AuthorsJavier Guenaga / Monika Ádori / Shridhar Bale / Swastik Phulera / Ioannis Zygouras / Fabian-Alexander Schleich / Xaquin Castro Dopico / Sashank Agrawal / Miyo Ota / Richard Wilson / Jocelyn Cluff / Tamar Dzvelaia / Marco Mandolesi / Wen-Hsin Lee / Agnes A Walsh / Mariane B Melo / Laurent Verkoczy / Darrell J Irvine / Martin Corcoran / Ian A Wilson / Diane Carnathan / Guido Silvestri / Andrew B Ward / Gabriel Ozorowski / Gunilla B Karlsson Hedestam / Richard T Wyatt /
PubMed AbstractAs a chronically replicating virus, HIV has evolved extreme sequence variability and effective shielding of functionally constrained spike protein determinants by host-derived glycans. Broadly ...As a chronically replicating virus, HIV has evolved extreme sequence variability and effective shielding of functionally constrained spike protein determinants by host-derived glycans. Broadly neutralizing antibodies, although rare, can be isolated from people living with HIV, revealing conserved envelope glycoprotein (Env) sites as key targets for vaccine development. One such target is the apex of the Env spike. Here we identify a vaccination strategy using heterologous HIV Env trimers covalently coupled to liposomes for multivalent display that resulted in the elicitation of cross-neutralizing HIV serum antibody responses in all trimer-liposome-immunized non-human primates. Critically, we isolated monoclonal antibodies from multiple macaques that cross-neutralize divergent HIV clinical isolates. High-resolution cryogenic electron microscopy structural analyses of monoclonal antibodies from four different macaques demonstrate that they target the Env trimer apex in a manner highly similar to that of the human-infection-elicited, apex-directed broadly neutralizing antibody PG9, representing a substantial advance in HIV vaccine development.
External linksNature / PubMed:42056526
MethodsEM (single particle) / X-ray diffraction
Resolution1.544 - 30.0 Å
Structure data

72009

9py5

EMDB-72009, PDB-9py5:
Q10M-055 Fab in complex with HIV-1 Env Q23 NFL TD CC3+
Method: EM (single particle) / Resolution: 3.5 Å

72031

9pyd

EMDB-72031, PDB-9pyd:
Q12QBM-007 Fab in complex with HIV-1 Env BG505 NFL TD CC3+
Method: EM (single particle) / Resolution: 3.3 Å

72033

9pyh

EMDB-72033, PDB-9pyh:
Q9M-023 Fab in complex with HIV-1 Env BG505 NFL TD CC3+
Method: EM (single particle) / Resolution: 3.3 Å

72035

9pyk

EMDB-72035, PDB-9pyk:
Q12BBM-069 Fab in complex with HIV-1 Env BG505 NFL TD CC3+
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-72735: HIV-1 Env Q23 NFL TD CC3+ in complex with NHP Q9 V2-apex polyclonal antibody Fabs isolated post-2 immunizations
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-72736: HIV-1 Env Q23 NFL TD CC3+ in complex with NHP Q10 V2-apex polyclonal antibody Fabs isolated post-2 immunizations
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-72737: HIV-1 Env Q23 NFL TD CC3+ in complex with NHP Q12 V2-apex polyclonal antibody Fabs isolated post-2 immunizations
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-72738: HIV-1 Env 16055 NFL TD CC2+ in complex with pooled NHP Q8-Q9-Q12 V2-apex polyclonal antibody Fabs isolated post-4 immunizations
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-72739: HIV-1 Env BG505 NFL TD CC3+ in complex with pooled NHP Q8-Q9-Q12 V2-apex polyclonal antibody Fabs isolated post-4 immunizations
Method: EM (single particle) / Resolution: 20.0 Å

EMDB-74449: Q7M-675 Fab in complex with HIV-1 Env WITO NFL TD CC3+
Method: EM (single particle) / Resolution: 4.3 Å

PDB-9pyn:
Crystal structure of HIV Apex fab Q9M-023
Method: X-RAY DIFFRACTION / Resolution: 2.34 Å

PDB-9pyy:
Crystal structure of HIV Apex Fab Q10M_055
Method: X-RAY DIFFRACTION / Resolution: 1.63 Å

PDB-9pz2:
Crystal structure of HIV Apex neutralizing Fab Q12QBM-007
Method: X-RAY DIFFRACTION / Resolution: 1.544 Å

PDB-9pz3:
Crystal structure of HIV Apex targeting neutralizing antibody Q12BBM-069
Method: X-RAY DIFFRACTION / Resolution: 1.79 Å

Chemicals

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

ChemComp-HOH:
WATER

Source
  • human immunodeficiency virus 1
  • macaca mulatta (Rhesus monkey)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 / macaque / non-human primate / NHP / V2-apex / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex / vaccine / IMMUNE SYSTEM / HIV / Apex targeting neutralizing antibody / Apex mAb / NHPs / HIV Apex neutralizing antibody / Apex neutralizing antibody

+
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