[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

TitleNeutralizing Antibody Responses Induced by HIV-1 Envelope Glycoprotein SOSIP Trimers Derived from Elite Neutralizers.
Journal, issue, pagesJ Virol, Vol. 94, Issue 24, Year 2020
Publish dateNov 23, 2020
AuthorsAnna Schorcht / Tom L G M van den Kerkhof / Christopher A Cottrell / Joel D Allen / Jonathan L Torres / Anna-Janina Behrens / Edith E Schermer / Judith A Burger / Steven W de Taeye / Alba Torrents de la Peña / Ilja Bontjer / Stephanie Gumbs / Gabriel Ozorowski / Celia C LaBranche / Natalia de Val / Anila Yasmeen / Per Johan Klasse / David C Montefiori / John P Moore / Hanneke Schuitemaker / Max Crispin / Marit J van Gils / Andrew B Ward / Rogier W Sanders /
PubMed AbstractThe induction of broadly neutralizing antibodies (bNAbs) is a major goal in vaccine research. HIV-1-infected individuals that develop exceptionally strong bNAb responses, termed elite neutralizers, ...The induction of broadly neutralizing antibodies (bNAbs) is a major goal in vaccine research. HIV-1-infected individuals that develop exceptionally strong bNAb responses, termed elite neutralizers, can inform vaccine design by providing blueprints for the induction of similar bNAb responses. We describe a new recombinant native-like envelope glycoprotein (Env) SOSIP trimer, termed AMC009, based on the viral founder sequences of an elite neutralizer. The subtype B AMC009 SOSIP protein formed stable native-like trimers that displayed multiple bNAb epitopes. Overall, its structure at 4.3-Å resolution was similar to that of BG505 SOSIP.664. The AMC009 trimer resembled one from a second elite neutralizer, AMC011, in having a dense and complete glycan shield. When tested as immunogens in rabbits, the AMC009 trimers did not induce autologous neutralizing antibody (NAb) responses efficiently while the AMC011 trimers did so very weakly, outcomes that may reflect the completeness of their glycan shields. The AMC011 trimer induced antibodies that occasionally cross-neutralized heterologous tier 2 viruses, sometimes at high titer. Cross-neutralizing antibodies were more frequently elicited by a trivalent combination of AMC008, AMC009, and AMC011 trimers, all derived from subtype B viruses. Each of these three individual trimers could deplete the NAb activity from the rabbit sera. Mapping the polyclonal sera by electron microscopy revealed that antibodies of multiple specificities could bind to sites on both autologous and heterologous trimers. These results advance our understanding of how to use Env trimers in multivalent vaccination regimens and the immunogenicity of trimers derived from elite neutralizers. Elite neutralizers, i.e., individuals who developed unusually broad and potent neutralizing antibody responses, might serve as blueprints for HIV-1 vaccine design. Here, we studied the immunogenicity of native-like recombinant envelope glycoprotein (Env) trimers based on viral sequences from elite neutralizers. While immunization with single trimers from elite neutralization did not recapitulate the breadth and potency of neutralization observed in these infected individuals, a combination of three subtype B Env trimers from elite neutralizers resulted in some neutralization breadth within subtype B viruses. These results should guide future efforts to design vaccines to induce broadly neutralizing antibodies.
External linksJ Virol / PubMed:32999024 / PubMed Central
MethodsEM (single particle)
Resolution4.25 - 36.0 Å
Structure data

EMDB-21258, PDB-6vo3:
AMC009 SOSIP.v4.2 in complex with PGV04 Fab
Method: EM (single particle) / Resolution: 4.25 Å

EMDB-22434:
UA0068 week 38 Fabs in complex with REJO SOSIP.v4.2 D368R
Method: EM (single particle) / Resolution: 31.0 Å

EMDB-22435:
UA0088 week 38 Fabs in complex with SF162p3 SOSIP.v9
Method: EM (single particle) / Resolution: 28.0 Å

EMDB-22436:
UA0083 week 38 Fabs in complex with SF162p3 SOSIP.v9
Method: EM (single particle) / Resolution: 28.0 Å

EMDB-22437:
UA0089 week 38 Fabs in complex with AMCO11 SOSIP.v5.2
Method: EM (single particle) / Resolution: 34.0 Å

EMDB-22438:
UA0089 week 38 Fabs in complex with AMCO11 SOSIP.v5.2
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-22439:
UA0091 week 38 Fabs in complex with REJO SOSIP.v4.2 D368R
Method: EM (single particle) / Resolution: 30.0 Å

EMDB-22440:
UA0091 week 38 Fabs in complex with REJO SOSIP.v4.2 D368R
Method: EM (single particle) / Resolution: 36.0 Å

EMDB-22442:
UA0068 week 38 Fabs in complex with AMCO11 SOSIP.v5.2
Method: EM (single particle) / Resolution: 25.0 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

Source
  • human immunodeficiency virus 1
  • homo sapiens (human)
KeywordsIMMUNE SYSTEM / HIV / Env / antibody / VIRAL PROTEIN

+
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