8TQ6 | pdb_00008tq6

Crystal structure of Fab.B1.23.2 in complex with MHC-I (HLA-B*44:05)

• PDB DOI: https://doi.org/10.2210/pdb8TQ6/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct, Mus musculus
• Expression System: Escherichia coli BL21(DE3), Homo sapiens
• Mutation(s): No 


• Deposited: 2023-08-06 Released: 2025-02-05 
• Deposition Author(s): Jiang, J., Natarajan, K., Boyd, L.F., 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: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

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 

• PubMed: 41629525 
• DOI: https://doi.org/10.1038/s42003-026-09641-8
• Primary Citation of Related Structures:  
  8TQ6, 9D72, 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: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A2B1C1D1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 182.3 kDa 
• Atom Count: 12,516 
• Modeled Residue Count: 1,607 
• Deposited Residue Count: 1,616 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen B alpha chain (HLA-B*44:05)	A, C	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B
UniProt
Find proteins for Q860B7 (Homo sapiens) Explore Q860B7  Go to UniProtKB:  Q860B7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II antigen peptide	E, J [auth P]	9	synthetic construct	Mutation(s): 0
UniProt
Find proteins for Q9TQB0 (Homo sapiens) Explore Q9TQB0  Go to UniProtKB:  Q9TQB0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab B1.23.2 Heavy Chain	F, H	213	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab B1.23.2 Light Chain	G, I [auth L]	212	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.268 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.5	α = 90
b = 92.84	β = 90
c = 229.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-05 
Deposition Author(s): Jiang, J., Natarajan, K., Boyd, L.F., 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	--

Revision History  

• Version 1.0: 2025-02-05
  Type: Initial release
  
• Version 1.1: 2026-02-11
  Changes: Database references