9DL1 | pdb_00009dl1

Crystal Structure of HLA-A*02:01/NY-ESO-1 (SLLMWITQV) and a target specific TRACeR-I

• PDB DOI: https://doi.org/10.2210/pdb9DL1/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-10 Released: 2024-11-20 
• Deposition Author(s): Mallik, L., Du, H., Huang, P., Sgourakis, N.G.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Targeting peptide antigens using a multiallelic MHC I-binding system.

Du, H., Mallik, L., Hwang, D., Sun, Y., Kaku, C., Hoces, D., Sun, S.M., Ghinnagow, R., Carro, S.D., Phan, H.A.T., Gupta, S., Blackson, W., Lee, H., Choe, C.A., Dersh, D., Liu, J., Bell, B., Yang, H., Papadaki, G.F., Young, M.C., Zhou, E., El Nesr, G., Goli, K.D., Eisenlohr, L.C., Minn, A.J., Hernandez-Lopez, R.A., Jardine, J.G., Sgourakis, N.G., Huang, P.S.

(2025) Nat Biotechnol 43: 1683-1693

• PubMed: 39672954 
• DOI: https://doi.org/10.1038/s41587-024-02505-8
• Primary Citation Related Structures: 
  9DL1


• PubMed Abstract: 
  

  Identifying highly specific T cell receptors (TCRs) or antibodies against epitopic peptides presented by class I major histocompatibility complex (MHC I) proteins remains a bottleneck in the development of targeted therapeutics. Here, we introduce targeted recognition of antigen-MHC complex reporter for MHC I (TRACeR-I), a generalizable platform for targeting peptides on polymorphic HLA-A*, HLA-B* and HLA-C* allotypes while overcoming the cross-reactivity challenges of TCRs. Our TRACeR-MHC I co-crystal structure reveals a unique antigen recognition mechanism, with TRACeR forming extensive contacts across the entire peptide length to confer single-residue specificity at the accessible positions. We demonstrate rapid screening of TRACeR-I against a panel of disease-relevant HLAs with peptides derived from human viruses (human immunodeficiency virus, Epstein-Barr virus and severe acute respiratory syndrome coronavirus 2), and oncoproteins (Kirsten rat sarcoma virus, paired-like homeobox 2b and New York esophageal squamous cell carcinoma 1). TRACeR-based bispecific T cell engagers and chimeric antigen receptor T cells exhibit on-target killing of tumor cells with high efficacy in the low nanomolar range. Our platform empowers the development of broadly applicable MHC I-targeting molecules for research, diagnostic and therapeutic applications.

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Organizational Affiliation: 
• Department of Chemistry, Stanford University, Stanford, CA, USA.
Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA, USA.
Department of Bioengineering, Stanford University, Stanford, CA, USA.
Department of Genetics, Stanford University, Stanford, CA, USA.
Cancer Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
Biophysics Program, Stanford University, Stanford, CA, USA.
Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
Chan-Zuckerberg Biohub, San Francisco, CA, USA.
Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA. [e-mail].
Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. [e-mail].
Department of Chemistry, Stanford University, Stanford, CA, USA. [e-mail].
Department of Bioengineering, Stanford University, Stanford, CA, USA. [e-mail].
Biophysics Program, Stanford University, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A2B2C2D1E1 

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

Macromolecule Content 

• Total Structure Weight: 122.49 kDa 
• Atom Count: 8,899 
• Modeled Residue Count: 1,007 
• Deposited Residue Count: 1,034 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRACeR-I	A, D	132	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen, A-2 alpha chain	B, F	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for A0A5B8RNS7 (Homo sapiens) Explore A0A5B8RNS7  Go to UniProtKB:  A0A5B8RNS7

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	C, G	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cancer/testis antigen 1	E, H	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P78358 (Homo sapiens) Explore P78358  Go to UniProtKB:  P78358
PHAROS:  P78358 GTEx:  ENSG00000184033 ENSG00000268651

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	I [auth B], J [auth B], K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.421	α = 90
b = 95.614	β = 90
c = 259.703	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
BUSTER	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Mallik, L., Du, H., Huang, P., Sgourakis, N.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R01AI143997
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R35GM125034

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release
  
• Version 1.1: 2024-12-25
  Changes: Database references
• Version 1.2: 2025-10-29
  Changes: Database references