Cryo-EM structure of the ternary DARPin NY_1/HLA-A0201/NY-ESO1 complex. Determined by electron microscopy at 3.1 Å resolution. Released 28 May 2025.
Explore 9FE1 in 3D Show helices and sheets RCSB PDB PDBe
9FE1 contains 16 α-helices and 29 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3-12 | 10 | 1 |
| β-strand | 21-28 | 8 | 1 |
| β-strand | 31-37 | 7 | 1 |
| α-helix | 52-54 | 3 | |
| α-helix | 57-84 | 28 | |
| β-strand | 94-103 | 10 | 1 |
| β-strand | 109-118 | 10 | 1 |
| β-strand | 121-126 | 6 | 1 |
| β-strand | 133-135 | 3 | 1 |
| α-helix | 138-150 | 13 | |
| α-helix | 152-161 | 10 | |
| α-helix | 163-174 | 12 | |
| β-strand | 183 | 1 | 2 |
| α-helix | 184-185 | 2 | |
| β-strand | 186-192 | 7 | 3 |
| β-strand | 198-208 | 11 | 3 |
| β-strand | 209 | 1 | 2 |
| β-strand | 214-218 | 5 | 4 |
| β-strand | 223 | 1 | 4 |
| β-strand | 230 | 1 | 3 |
| β-strand | 234-235 | 2 | 3 |
| β-strand | 241-250 | 10 | 3 |
| β-strand | 258-262 | 5 | 4 |
| β-strand | 272-273 | 2 | 4 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 3 | 1 | 5 |
| β-strand | 6-11 | 6 | 6 |
| β-strand | 21-30 | 10 | 6 |
| β-strand | 31 | 1 | 5 |
| β-strand | 36-41 | 6 | 7 |
| β-strand | 44-45 | 2 | 7 |
| β-strand | 50-51 | 2 | 6 |
| β-strand | 55-56 | 2 | 6 |
| β-strand | 62-70 | 9 | 6 |
| β-strand | 78-83 | 6 | 7 |
| β-strand | 91-94 | 4 | 7 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 14-24 | 11 | |
| α-helix | 27-36 | 10 | |
| α-helix | 50-57 | 8 | |
| α-helix | 60-68 | 9 | |
| α-helix | 83-90 | 8 | |
| α-helix | 93-102 | 10 | |
| α-helix | 116-123 | 8 | |
| α-helix | 126-134 | 9 | |
| α-helix | 149-156 | 8 | |
| α-helix | 159-168 | 10 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| MHC class I antigen | A | protein | 291 | Homo sapiens | Q8WLS4 (AlphaFold model) |
| Beta-2-microglobulin | B | protein | 100 | Homo sapiens | P61769 (AlphaFold model) |
| Cancer/testis antigen 1 | C | protein | 9 | Homo sapiens | P78358 (AlphaFold model) |
| DARPin NY_1 | D | protein | 175 | synthetic construct |
>9FE1_1 MHC class I antigen (chains A) MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPGSGGSAWSHPQFEK
>9FE1_2 Beta-2-microglobulin (chains B) MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
>9FE1_3 Cancer/testis antigen 1 (chains C) SLLMWITQV
>9FE1_4 DARPin NY_1 (chains D) MRGSHHHHHHENLYFQGSDLGKKLLQAARAGQLDEVRELLKAGADVNAKDLIGVTPLHLA AFSGHLEIVEVLLKASADVNAKDVSGRTPLHVAAKHGHLEIVEVLLKAGADVNAKDLIGF TPLHLAAQFGHLEIVEVLLKAGADVNAQDKSGKTPADLAARAGHQDIAEVLQKAA
Development of DARPin T cell engagers for specific targeting of tumor-associated HLA/peptide complexes. Venetz-Arenas, N., Schulte, T., Muller, S. et al. iScience (2025) 28:113926-113926. DOI 10.1016/j.isci.2025.113926 · PubMed
Other PDB entries of the same protein (UniProt Q8WLS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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