Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.08 kDa 
• Atom Count: 3,481 
• Modelled Residue Count: 382 
• Deposited Residue Count: 383 
• Unique protein chains: 3

 7L1C

Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide

• PDB DOI: 10.2210/pdb7L1C/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli #1/H766, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-12-14 Released: 2022-03-23 
• Deposition Author(s): Ma, J., Baker, B.M.
• 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: 1.96 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA.

Chandran, S.S., Ma, J., Klatt, M.G., Dundar, F., Bandlamudi, C., Razavi, P., Wen, H.Y., Weigelt, B., Zumbo, P., Fu, S.N., Banks, L.B., Yi, F., Vercher, E., Etxeberria, I., Bestman, W.D., Da Cruz Paula, A., Aricescu, I.S., Drilon, A., Betel, D., Scheinberg, D.A., Baker, B.M., Klebanoff, C.A.

(2022) Nat Med 28: 946-957

• PubMed: 35484264 
• DOI: 10.1038/s41591-022-01786-3
• Primary Citation of Related Structures:  
  7L1B, 7L1C, 7L1D, 7RRG


• PubMed Abstract: 
  

Public neoantigens (NeoAgs) represent an elite class of shared cancer-specific epitopes derived from recurrently mutated driver genes. Here we describe a high-throughput platform combining single-cell transcriptomic and T cell receptor (TCR) sequencing to establish whether mutant PIK3CA, among the most frequently genomically altered driver oncogenes, generates an immunogenic public NeoAg. Using this strategy, we developed a panel of TCRs that recognize an endogenously processed neopeptide encompassing a common PIK3CA hotspot mutation restricted by the prevalent human leukocyte antigen (HLA)-A*03:01 allele. Mechanistically, immunogenicity to this public NeoAg arises from enhanced neopeptide/HLA complex stability caused by a preferred HLA anchor substitution. Structural studies indicated that the HLA-bound neopeptide presents a comparatively 'featureless' surface dominated by the peptide's backbone. To bind this epitope with high specificity and affinity, we discovered that a lead TCR clinical candidate engages the neopeptide through an extended interface facilitated by an unusually long CDR3β loop. In patients with diverse malignancies, we observed NeoAg clonal conservation and spontaneous immunogenicity to the neoepitope. Finally, adoptive transfer of TCR-engineered T cells led to tumor regression in vivo in mice bearing PIK3CA-mutant tumors but not wild-type PIK3CA tumors. Together, these findings establish the immunogenicity and therapeutic potential of a mutant PIK3CA-derived public NeoAg.

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Organizational Affiliation: 

Cell Therapy Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A alpha chain	A	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439  Go to UniProtKB:  P04439
PHAROS:  P04439

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mutant PIK3CA peptide	C	9	Homo sapiens	Mutation(s): 1  Gene Names: PIK3CA EC: 2.7.1.137 (UniProt), 2.7.1.153 (UniProt), 2.7.11.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336  Go to UniProtKB:  P42336
PHAROS:  P42336

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT (Subject of Investigation/LOI)	F [auth A], G [auth A], K [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 0.205 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 155.72	α = 90
b = 155.72	β = 90
c = 85.66	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Ma, J., Baker, B.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI129543

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references
• Version 1.2: 2022-05-25
  Changes: Database references