9MIN | pdb_00009min

Structure of a designed minibinder to NYESO1-A*02:01

PDB DOI: https://doi.org/10.2210/pdb9MIN/pdb

Classification: DE NOVO PROTEIN
Organism(s): Homo sapiens, synthetic construct, Lama glama
Expression System: Escherichia coli, Homo sapiens
Mutation(s): Yes

Deposited: 2024-12-13 Released: 2025-08-06
Deposition Author(s): Jude, K.M., Householder, K.D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.267 (Depositor), 0.267 (DCC)
R-Value Work:
0.255 (Depositor), 0.255 (DCC)
R-Value Observed:
0.255 (Depositor)

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

De novo design and structure of a peptide-centric TCR mimic binding module.

Householder, K.D., Xiang, X., Jude, K.M., Deng, A., Obenaus, M., Zhao, Y., Wilson, S.C., Chen, X., Wang, N., Garcia, K.C.

(2025) Science 389: 375-379

PubMed: 40705894 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.adv3813
Primary Citation Related Structures:
9MIN

PubMed Abstract:
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 K _d = 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.

Organizational Affiliation

Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.

Macromolecule Content

Total Structure Weight: 148.05 kDa
Atom Count: 10,482
Modeled Residue Count: 1,258
Deposited Residue Count: 1,286
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I antigen	A, F	278	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A
UniProt
Find proteins for Q53Z42 (Homo sapiens) Explore Q53Z42 Go to UniProtKB: Q53Z42
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q53Z42
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, G	101	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
Cancer/testis antigen 1	C, H	9	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P78358 (Homo sapiens) Explore P78358 Go to UniProtKB: P78358
PHAROS: P78358 GTEx: ENSG00000184033 ENSG00000268651
Entity Groups
UniProt Group	P78358
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
designed minibinder KH46	D, I	136	synthetic construct	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
nanobody AD01	E, J	119	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File 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 O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth E] SDF format, chain U [auth F] SDF format, chain V [auth F] SDF format, chain W [auth F] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth J] 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 O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] MOL2 format, chain V [auth F] MOL2 format, chain W [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth J] 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 O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth E] mmCIF format, chain U [auth F] mmCIF format, chain V [auth F] mmCIF format, chain W [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth J]	K [auth A] L [auth A] M [auth A] N [auth A] O [auth A] K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth E], U [auth F], V [auth F], W [auth F], X [auth G], Y [auth G], Z [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth J] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth J]