9MIN image
Deposition Date 2024-12-13
Release Date 2025-08-06
Last Version Date 2025-08-06
Entry Detail
PDB ID:
9MIN
Keywords:
Title:
Structure of a designed minibinder to NYESO1-A*02:01
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
synthetic construct (Taxon ID: 32630)
Lama glama (Taxon ID: 9844)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.05 Å
R-Value Free:
0.26
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:HLA class I antigen
Gene (Uniprot):HLA-A
Mutagens:insertion of MG at N-terminus - cloning artifact
Chain IDs:A, F
Chain Length:278
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Beta-2-microglobulin
Gene (Uniprot):B2M
Mutagens:insertion of MG at N-terminus - cloning artifact
Chain IDs:B, G
Chain Length:101
Number of Molecules:2
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Cancer/testis antigen 1
Gene (Uniprot):CTAG1A, CTAG1B
Mutagens:C9V
Chain IDs:C, H
Chain Length:9
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:designed minibinder KH46
Chain IDs:D, I
Chain Length:136
Number of Molecules:2
Biological Source:synthetic construct
Polymer Type:polypeptide(L)
Molecule:nanobody AD01
Chain IDs:E, J
Chain Length:119
Number of Molecules:2
Biological Source:Lama glama
Ligand Molecules
Primary Citation
De novo design and structure of a peptide-centric TCR mimic binding module.
Science 389 375 379 (2025)
PMID: 40705894 DOI: 10.1126/science.adv3813

Abstact

T cell receptor (TCR) mimics offer a promising platform for tumor-specific targeting of peptide-major histocompatibility complex (pMHC) in cancer immunotherapy. In this study, we designed a de novo α-helical TCR mimic (TCRm) specific for the NY-ESO-1 peptide presented by human leukocyte antigen (HLA)-A*02, achieving high on-target specificity with nanomolar affinity (dissociation constant Kd = 9.5 nM). The structure of the TCRm-pMHC complex at 2.05-Å resolution revealed a rigid TCR-like docking mode with an unusual degree of focus on the up-facing NY-ESO-1 side chains, suggesting the potential for reduced off-target reactivity. Indeed, a structure-informed in silico screen of 14,363 HLA-A*02 peptides correctly predicted two off-target peptides, yet our TCRm maintained peptide selectivity and cytotoxicity as a T cell engager. These results represent a path for precision targeting of tumor antigens with peptide-focused α-helical TCR mimics.

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Primary Citation of related structures