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Structure paper

TitleIdentification of IOMA-class neutralizing antibodies targeting the CD4-binding site on the HIV-1 envelope glycoprotein.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 4515, Year 2022
Publish dateAug 3, 2022
AuthorsJelle van Schooten / Elinaz Farokhi / Anna Schorcht / Tom L G M van den Kerkhof / Hongmei Gao / Patricia van der Woude / Judith A Burger / Tim G Rijkhold Meesters / Tom Bijl / Riham Ghalaiyini / Hannah L Turner / Jessica Dorning / Barbera D C van Schaik / Antoine H C van Kampen / Celia C Labranche / Robyn L Stanfield / Devin Sok / David C Montefiori / Dennis R Burton / Michael S Seaman / Gabriel Ozorowski / Ian A Wilson / Rogier W Sanders / Andrew B Ward / Marit J van Gils /
PubMed AbstractA major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope ...A major goal of current HIV-1 vaccine design efforts is to induce broadly neutralizing antibodies (bNAbs). The VH1-2-derived bNAb IOMA directed to the CD4-binding site of the HIV-1 envelope glycoprotein is of interest because, unlike the better-known VH1-2-derived VRC01-class bNAbs, it does not require a rare short light chain complementarity-determining region 3 (CDRL3). Here, we describe three IOMA-class NAbs, ACS101-103, with up to 37% breadth, that share many characteristics with IOMA, including an average-length CDRL3. Cryo-electron microscopy revealed that ACS101 shares interactions with those observed with other VH1-2 and VH1-46-class bNAbs, but exhibits a unique binding mode to residues in loop D. Analysis of longitudinal sequences from the patient suggests that a transmitter/founder-virus lacking the N276 glycan might have initiated the development of these NAbs. Together these data strengthen the rationale for germline-targeting vaccination strategies to induce IOMA-class bNAbs and provide a wealth of sequence and structural information to support such strategies.
External linksNat Commun / PubMed:35922441 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.73 - 25.0 Å
Structure data

14474

7z3a

EMDB-14474, PDB-7z3a:
AMC009 SOSIPv5.2 in complex with Fabs ACS101 and ACS124
Method: EM (single particle) / Resolution: 3.95 Å

EMDB-14475: AMC009 SOSIPv5.2 + ACS101 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-14476: AMC009 SOSIPv5.2 in complex with ACS102 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-14477: AMC009 SOSIPv5.2 in complex with ACS103 Fab
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-14478: AMC009 SOSIPv5.2 in complex with ACS124 Fab
Method: EM (single particle) / Resolution: 25.0 Å

PDB-7u04:
IOMA class antibody ACS101
Method: X-RAY DIFFRACTION / Resolution: 2.31 Å

PDB-7u0k:
IOMA class antibody Fab ACS124
Method: X-RAY DIFFRACTION / Resolution: 1.73 Å

Chemicals

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-HOH:
WATER / Water

ChemComp-NHE:
2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / pH buffer*YM / CHES (buffer)

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

Source
  • human immunodeficiency virus 1
  • homo sapiens (human)
KeywordsIMMUNE SYSTEM / Antibody / IOMA / HIV / STRUCTURAL PROTEIN / VIRAL PROTEIN / HIV-1 / antibodies / CD4-binding site / gp41-gp120 interface

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