9MIN | pdb_00009min

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


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

  • DOI: https://doi.org/10.1126/science.adv3813
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I antigen
A, F
278Homo sapiensMutation(s): 0 
Gene Names: HLA-A
UniProt
Find proteins for Q53Z42 (Homo sapiens)
Explore Q53Z42 
Go to UniProtKB:  Q53Z42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53Z42
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, G
101Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cancer/testis antigen 1
C, H
9Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P78358 (Homo sapiens)
Explore P78358 
Go to UniProtKB:  P78358
PHAROS:  P78358
Entity Groups  
UniProt GroupP78358
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
designed minibinder KH46
D, I
136synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody AD01
E, J
119Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
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
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.452α = 90
b = 98.536β = 90
c = 155.743γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5R01AI103867-08

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-06
    Type: Initial release