8TQ5 | pdb_00008tq5

Crystal structure of Fab DX17 in complex with MHC-I (HLA-B*44:05)

• PDB DOI: https://doi.org/10.2210/pdb8TQ5/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli BL21(DE3), Escherichia coli, 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: 2.30 Å
• R-Value Free: 
  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Antibody Mediated Inhibition of HLA/LILR Interactions Breaks Innate Immune Tolerance and Induces Antitumor Immunity.

Panda, A.K., Natarajan, K., Sinha, S., Jiang, J., Chempati, S., Boyd, L.F., Desai, P.P., Buszko, M., Kim, Y.H., Kazmi, S., Fisk, B., Teke, M.E., Larrain, C.M., Remmert, K., Blakely, A.M., Douagi, I., Hernandez, J.M., Margulies, D.H., Shevach, E.M.

(2025) Cancer Immunol Res 

• PubMed: 41032026 
• DOI: https://doi.org/10.1158/2326-6066.CIR-25-0343
• Primary Citation of Related Structures:  
  8TQ5


• PubMed Abstract: 
  

  Immune check-point blockade for the treatment of malignancies has been focused on reversing inhibitory pathways in T lymphocytes. Natural killer (NK) cells are a potent innate defense against tumors and virally infected cells, but their therapeutic manipulation for anti-cancer immunity has been inadequately explored. Considerable attention has been focused on approaches to blocking inhibitory receptors on NK and myeloid cells. Most effort has been directed to the killer immunoglobulin-like receptors (KIR) and CD94/NKG2A on NK cells. Another set of receptors with similar function in both NK cells and myeloid cells is the leukocyte immunoglobulin like receptors (LILR) that interact with a wide variety of HLA molecules. Using pan-anti-HLA mAbs that recognize a conserved epitopic region on HLA also seen by LILR, we investigated their functional effects in several models of tumor immunity. The pan-anti-HLA-mAbs blocked the binding of most LILRs, did not block killer cell immunoglobulin-like receptors (KIR) or CD94/NKG2A/C or TCR recognition. They also activated dysfunctional NK cells explanted from a variety of human cancers, and resulted in enhancement of tumor immunity in humanized mice. The mAbs also exert direct anti-tumor effects. These results suggest that activation of innate immunity via disruption of HLA/LILR interactions is a potent approach for control of both primary tumors and potentially tumor metastases.

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Organizational Affiliation: 
• National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States.
National Institutes of Health, United States.
National Cancer Institute, United States.
National Institutes of Health, Bethesda, MD, United States.
National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States.
NIAID, United States.
The University of Texas Southwestern Medical Center, United States.
National Cancer Institute, Bethesda, Maryland, United States.
National Cancer Institute, Bethesda, MD, United States.

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)

Macromolecule Content 

• Total Structure Weight: 92.47 kDa 
• Atom Count: 6,609 
• Modeled Residue Count: 810 
• Deposited Residue Count: 818 
• 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	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	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	C [auth P]	9	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DPA1
UniProt
Find proteins for Q9TQB0 (Homo sapiens) Explore Q9TQB0  Go to UniProtKB:  Q9TQB0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab DX17 H-chain	D [auth H]	221	Mus musculus	Mutation(s): 0
Glycosylation
Glycosylation Sites: 1

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab DX17 L-chain	E [auth L]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.115	α = 90
b = 104.427	β = 90
c = 131.49	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: 2025-10-08
  Changes: Database references