9OA9 | pdb_00009oa9

CryoEM structure of anti-MHC-I mAb B1.23.2 Fc domains

• PDB DOI: https://doi.org/10.2210/pdb9OA9/pdb
• EM Map EMD-70276: EMDB EMDataResource

• Classification: ANTITUMOR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-04-20 Released: 2026-02-04 
• Deposition Author(s): Jiang, J., Natarajan, K., Margulies, D.H.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structural mechanism of anti-MHC-I antibody blocking of inhibitory NK cell receptors in tumor immunity.

Jiang, J., Panda, A.K., Natarajan, K., Lei, H., Sharma, S., Boyd, L.F., Towler, R.R., Chempati, S., Ahmad, J., Morton, A.J., Lang, Z.C., Sun, Y., Sgourakis, N., Meier-Schellersheim, M., Huang, R.K., Shevach, E.M., Margulies, D.H.

(2026) Commun Biol 9

• PubMed: 41629525 
• DOI: https://doi.org/10.1038/s42003-026-09641-8
• Primary Citation Related Structures: 
  8TQ6, 9D73, 9D74, 9OA9


• PubMed Abstract: 
  

  Anti-major histocompatibility complex class I (MHC-I) mAbs can stimulate immune responses to tumors and infections by blocking suppressive signals delivered via various immune inhibitory receptors. To understand such functions, we determined the structure of a highly cross-reactive anti-human MHC-I mAb, B1.23.2, in complex with the MHC-I molecule HLA-B*44:05 by both cryo-electron microscopy (cryo-EM) and X-ray crystallography. Structural models determined by the two methods were essentially identical revealing that B1.23.2 binds a conserved region on the α2 ₁ helix that overlaps the killer immunoglobulin-like receptor (KIR) binding site. Structural comparison to KIR/HLA complexes reveals a mechanism by which B1.23.2 blocks inhibitory receptor interactions, leading to natural killer (NK) cell activation. B1.23.2 treatment of the human KLM-1 pancreatic cancer model in humanized (NSG-IL15) mice provides evidence of suppression of tumor growth. Such anti-MHC-I mAb that block inhibitory KIR/HLA interactions may prove useful for tumor immunotherapy.

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Organizational Affiliation: 
• Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].
Cellular Immunology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Research Technology Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Computational Systems Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Fred and Pamela Buffett Cancer Center and Eppley Institute for Cancer Research, Omaha, NE, USA.
Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Cellular Immunology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].
Molecular Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 99.24 kDa 
• Atom Count: 3,676 
• Modeled Residue Count: 550 
• Deposited Residue Count: 886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-MHC-I mAb B1.23.2 Fc domains H-chain	A [auth J], B [auth K]	443	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth X]	6		N-Glycosylation

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth Y]	6		N-Glycosylation

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.44 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3
MODEL REFINEMENT	PHENIX	1.19.2-4158

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-02-04 
Deposition Author(s): Jiang, J., Natarajan, K., Margulies, D.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	Intramural

Revision History  

• Version 1.0: 2026-02-04
  Type: Initial release
  
• Version 1.1: 2026-02-11
  Changes: Data collection, Database references
• Version 1.2: 2026-03-18
  Changes: Data collection, Database references