Cryo-EM structure of the ternary DARPin NY_1/HLA-A0201/NY-ESO1 complex.

2025-12-10 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update PDBe PDBe 2024-05-17 2025-05-28 2025-05-28 2025-12-10 Knut and Alice Wallenberg Foundation Sweden Cancerfonden Sweden Swedish Research Council Sweden Cryo-EM structure of the ternary DARPin NY_1/HLA-A0201/NY-ESO1 complex. Schulte T Wallden K Carroni M Sandalova T Walser M Mueller S Venetz N Achour A DARPin targeting MHC molecules in complex with tumor-associated peptide antigens, IMMUNE SYSTEM Venetz-Arenas N Schulte T Muller S Wallden K Fischer S Resink T Kadri N Paladino M Pina N Radom F Villemagne D Bruckmaier S Cornelius A Hospodarsch T Alici E Ljunggren HG Chambers BJ Han X Sun R Carroni M Levitsky V Sandalova T Walser M Achour A Development of DARPin T cell engagers for specific targeting of tumor-associated HLA/peptide complexes. Iscience US 28 113926 113926 2025 41321628 doi:10.1016/j.isci.2025.113926 2589-0042 9fe1 FULLOVERLAP PDB 9EPA unspecified

Crystal structure of NY_1

EMDB EMD-50336 associated EM volume

Ternary complex formed between the DARPin NY_1 and HLA-A0201/hb2m/NY-ESO1_157-165(9V) Ternary complex formed between the DARPin NY_1 and HLA-A0201/hb2m/NY-ESO1_157-165(9V) 0 1 2 3 4

Size-exclusion chromatography (SEC) was used to purify refolded complexes of HLA-A0201 with human beta-2-microglobulin (hb2m) and the peptide NY-ESO1157-165(9V). Strep-Tactin Superflow high capacity columns (1 mL, IBA lifescience) run in 20 mM HEPES, 300 mM NaCl pH 7.5 were used for further purification. After a column wash, the protein was eluted using the same buffer supplemented with 2.5 mM desthiobiotin. TEV-cleaved DARPin NY_1 was reverse-purified via IMAC and the monomer was isolated from Superdex 200 equilibrated in 20 mM HEPES, 150 mM NaCl pH 7.5. For cross-linking, HLA-A0201/NY-ESO1157-165(9V) was mixed in a 1:2 molar ratio with NY_1, concentrated to an absorbance at 280 nm (Abs280) of 2.3, and incubated for 45 min in 25 mM HEPES, 150 mM NaCl, supplemented with 1.4 mM BS(PEG)5 (BS5) (ThermoScientific). The cross-linker was quenched by addition of 25 mM Tris. Samples for grid screening were isolated from Superdex 200 GL 10/300 SEC in 25 mM HEPES, 150 mM NaCl, pH 7.4, and concentrated to Abs280 values of 2.

Homo sapiens 0.06 MHC class I antigen Homo sapiens 0.033541047 1 Escherichia coli LEVO MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLG TLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAY LEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPGSGGSAWSHPQFEK Q8WLS4 Beta-2-microglobulin Homo sapiens 0.011879355999999999 1 Escherichia coli LEVO MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYA CRVNHVTLSQPKIVKWDRDM P61769 Cancer/testis antigen 1 Homo sapiens 0.001090335 1 LEVO SLLMWITQV P78358 DARPin NY_1 synthetic construct 0.018596216999999998 1 Escherichia coli LEVO MRGSHHHHHHENLYFQGSDLGKKLLQAARAGQLDEVRELLKAGADVNAKDLIGVTPLHLAAFSGHLEIVEVLLKASADVN AKDVSGRTPLHVAAKHGHLEIVEVLLKAGADVNAKDLIGFTPLHLAAQFGHLEIVEVLLKAGADVNAQDKSGKTPADLAA RAGHQDIAEVLQKAA singleParticle particle 0.5 7.4

25 mM HEPES, 150 mM NaCl, pH 7.4

ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.6 2.5 130000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1 10855 2.3 57.5 1 7726585 cryoSPARC 3.3.1 PHASE FLIPPING AND AMPLITUDE CORRECTION C1 FOURIER SPACE 3.1 FSC 0.143 CUT-OFF cryoSPARC 3.3.1 204743 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 MAXIMUM LIKELIHOOD cryoSPARC 3.3.1 1 cryoSPARC 3.3.1 emd_50336.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 256 256 256 0 0 0 256 256 256 249.6 249.6 249.6 90.0 90.0 90.0 Z Y X -26.410246000000001 59.019302000000003 -0.000000000000989 1.0 0.975 0.975 0.975 12.0 AUTHOR ::::EMDATABANK.org::::EMD-50336:::: Phenix auto-sharpened, with model 1S9W PDB experimental model Other experimental model

NY_1 crystal structure, PDB code given in publication

The crystal structures of NY_1 and HLA-A0201/NY-ESO1 (PDB 1S9W) were placed into the initial map in ChimeraX. The model was iteratively refined by model building in Coot and ChimeraX-Isolde, as well as Phenix real space refinement with integrated amber force field with Ramachandran, secondary structure and reference structure restraints

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