Cryo-EM and X-ray structures of an anti-MHC-I monoclonal antibody/H2-Kb complex reveal the basis of conformational dependence and allelic specificity
- 1NIAID/NIH
Abstract
Monoclonal antibodies (mAbs) directed against MHC class I molecules (MHC-I) have been invaluable for a host of functions including tissue typing for transplantation, exploration of immune activation, and probing molecular structure and dynamics. We previously studied a set of murine mAbs directed against MHC-I to characterize their domain and allele specificity and demonstrated the consistency of structural identification of epitopes with prior mapping studies. Here, we report cryo-EM and X-ray crystal structures of a novel mAb (AF6-88.5) in complex with the mouse MHC-I molecule H2-Kb. We characterize the conformational epitope that is sensitive to polymorphic amino acid residues in the MHC-I extracellular domains. The structure of the mAb/MHC-I complex reveals contacts of the mAb to residues of the 2, 3, and {beta}2m domains and comparison to the unliganded mAb shows slight adjustments of the mAb CDRH3 and CDRL3 loops to accommodate the epitope surface. The structurally identified site overlaps with that seen by some coreceptors and immunoevasins. Amino acid sequence alignments and site-directed mutagenesis of H2-Kb, H2-Db, and {beta}2m explain the allelic specificity. These results emphasize the remarkable ability of antibodies to bind conformationally defined epitopes with exquisite discrimination and the contribution of MHC-I polymorphisms to antigenicity.
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BibTeX
@misc{jiang2026cryoem,
title = {{Cryo-EM and X-ray structures of an anti-MHC-I monoclonal antibody/H2-Kb complex reveal the basis of conformational dependence and allelic specificity}},
author = {j. Jiang and K. Natarajan and R. Towler and L. F. Boyd and A. B. Lupatkin and R. K. Huang and D. H. Margulies},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.11.750949},
url = {https://www.biorxiv.org/content/10.64898/2026.09.11.750949v1},
note = {CC0},
}
RIS
TY - UNPB
TI - Cryo-EM and X-ray structures of an anti-MHC-I monoclonal antibody/H2-Kb complex reveal the basis of conformational dependence and allelic specificity
AU - j. Jiang
AU - K. Natarajan
AU - R. Towler
AU - L. F. Boyd
AU - A. B. Lupatkin
AU - R. K. Huang
AU - D. H. Margulies
PY - 2026
DA - 2026/09/11
PB - bioRxiv
DO - 10.64898/2026.09.11.750949
UR - https://www.biorxiv.org/content/10.64898/2026.09.11.750949v1
AB - Monoclonal antibodies (mAbs) directed against MHC class I molecules (MHC-I) have been invaluable for a host of functions including tissue typing for transplantation, exploration of immune activation, and probing molecular structure and dynamics. We previously studied a set of murine mAbs directed against MHC-I to characterize their domain and allele specificity and demonstrated the consistency of structural identification of epitopes with prior mapping studies. Here, we report cryo-EM and X-ray crystal structures of a novel mAb (AF6-88.5) in complex with the mouse MHC-I molecule H2-Kb. We characterize the conformational epitope that is sensitive to polymorphic amino acid residues in the MHC-I extracellular domains. The structure of the mAb/MHC-I complex reveals contacts of the mAb to residues of the 2, 3, and {beta}2m domains and comparison to the unliganded mAb shows slight adjustments of the mAb CDRH3 and CDRL3 loops to accommodate the epitope surface. The structurally identified site overlaps with that seen by some coreceptors and immunoevasins. Amino acid sequence alignments and site-directed mutagenesis of H2-Kb, H2-Db, and {beta}2m explain the allelic specificity. These results emphasize the remarkable ability of antibodies to bind conformationally defined epitopes with exquisite discrimination and the contribution of MHC-I polymorphisms to antigenicity.
ER -