9OBF | pdb_00009obf

Crystal structure of HLA*02:01 with the 11-mer TP53 peptide GLAPPQHLIRV

PDB DOI: https://doi.org/10.2210/pdb9OBF/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-22 Released: 2026-06-24
Deposition Author(s): Tan, K., Mallis, R.J., Reinherz, E.L.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free:
0.212 (Depositor), 0.211 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Cancers modulate processing and presentation of p53 neoantigens to evade T cell detection.

Haratani, K., Reinhold, B., Duke-Cohan, J.S., Fahey, C.G., Tan, K., Mallis, R.J., Gusev, A., Kehl, K.L., Luo, J., Karmazyn, A., Holliday, E.L., Masi, D.J., Zienkiewicz, K.J., Hennessey, C.J., Blasco, R.B., Thai, T.C., Gibbons, G.M., Kivlehan, S., Lizotte, P., Paweletz, C.P., Aguirre, A.J., Ligon, K.L., Chiarle, R., Lang, M.J., Barbie, D.A., Reinherz, E.L.

(2026) Immunity 59: 2789

PubMed: 42753739 Search on PubMed
DOI: https://doi.org/10.1016/j.immuni.2026.08.011
Primary Citation Related Structures:
9EIQ, 9EJD, 9EK4, 9OBF, 9YZH

PubMed Abstract:
TP53 mutations occur early in malignant transformation as truncal events in tumor evolution and are therefore generally present in all descendant tumor cells, creating an immunological vulnerability. Here, we examined the immunogenicity and antigenicity of p53 neoantigens emerging from these truncal mutations. Comprehensive immunopeptidomics revealed that hotspot mutations in human tumors preferentially localize to p53 regions resistant to antigen processing, thereby avoiding display altogether. Moreover, for neoantigens presentable by HLA-A ^∗02:01 or HLA-B ^∗07:02 and structurally divergent from corresponding wild-type p53 peptide-HLA complexes, clinical tumors commonly lacked the relevant presenting HLA allele. Tumor cells further resisted T cell killing through increased activity of the aminopeptidase ERAP1, preventing display of high-affinity HLA-A ^∗02:01 complexes containing an immunogenic p53 ^I195F-derived 11-mer, or by expressing low-affinity HLA-A ^∗02:01 complexes containing a p53 ^R175H-derived 9-mer with poor antigenicity despite high-quality human TCRs. These findings define mechanisms by which tumors restrict targetable truncal neoantigen display and suggest immunopeptidome shift strategies to circumvent immune escape.

Organizational Affiliation

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA.

Structural Biology Center, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 S. Cass Avenue, Lemont, IL 60439, USA.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Dermatology, Harvard Medical School, Boston, MA, USA.

Division of Population Sciences, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.

Department of Pathology, Boston Children's Hospital, Boston, MA, USA.

Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA.

Department of Pathology, Dana-Farber Cancer Institute, Boston, MA, USA.

Department of Pathology, Boston Children's Hospital, Boston, MA, USA; Department of Molecular Biotechnology and Health Sciences, University of Torino, 10125 Torino, Italy; Division of Hematopathology, IEO European Institute of Oncology IRCCS, Milan, Italy.

Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA. Electronic address: david_barbie@dfci.harvard.edu.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA. Electronic address: ellis_reinherz@dfci.harvard.edu.

Macromolecule Content

Total Structure Weight: 91.26 kDa
Atom Count: 6,377
Modeled Residue Count: 774
Deposited Residue Count: 776
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D	277	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A*02:01
UniProt
Find proteins for Q861F7 (Homo sapiens) Explore Q861F7 Go to UniProtKB: Q861F7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q861F7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Cellular tumor antigen p53	C, F	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens) Explore P04637 Go to UniProtKB: P04637
PHAROS: P04637 GTEx: ENSG00000141510
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04637
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain P [auth D] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth B], P [auth D], Q [auth D], R [auth D], S [auth D], T [auth D], U [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.212 (Depositor), 0.211 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.13	α = 90
b = 161.13	β = 90
c = 330.28	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data scaling
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Tan, K.

Mallis, R.J.

Reinherz, E.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01CA265928
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P01AI143565
National Institutes of Health/Office of the Director	United States	S10OD030394