Cryo-EM structure of a de-novo designed binder NY1-B04 in complex with HLA-A*02:01 and NY-ESO-1-derived peptide SLLMWITQC. Determined by electron microscopy at 3.8 Å resolution. Released 23 Jul 2025.
Explore 9NNF in 3D Show helices and sheets RCSB PDB PDBe
9NNF contains 15 α-helices and 25 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 |
|---|---|---|---|
| α-helix | 11-24 | 14 | |
| α-helix | 30-50 | 21 | |
| α-helix | 59-83 | 25 | |
| α-helix | 88-109 | 22 | |
| α-helix | 113-144 | 32 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 148-157 | 10 | 1 |
| α-helix | 165 | 1 | |
| β-strand | 166-173 | 8 | 1 |
| β-strand | 176-180 | 5 | 1 |
| β-strand | 191-192 | 2 | 1 |
| α-helix | 202-230 | 29 | |
| β-strand | 239-248 | 10 | 1 |
| β-strand | 254-264 | 11 | 1 |
| β-strand | 266-271 | 6 | 1 |
| β-strand | 278-280 | 3 | 1 |
| α-helix | 283-294 | 12 | |
| α-helix | 298-303 | 6 | |
| α-helix | 304-308 | 5 | |
| α-helix | 309-319 | 11 | |
| α-helix | 321-324 | 4 | |
| α-helix | 328-330 | 3 | |
| β-strand | 333-339 | 7 | 2 |
| β-strand | 343-350 | 8 | 2 |
| β-strand | 359-363 | 5 | 3 |
| β-strand | 373-375 | 3 | 2 |
| α-helix | 376-378 | 3 | |
| β-strand | 379-380 | 2 | 4 |
| β-strand | 386-387 | 2 | 4 |
| β-strand | 388-394 | 7 | 2 |
| β-strand | 403-407 | 5 | 3 |
| β-strand | 415-418 | 4 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 429-433 | 5 | 5 |
| β-strand | 443-449 | 7 | 5 |
| β-strand | 457-463 | 7 | 6 |
| β-strand | 466 | 1 | 6 |
| β-strand | 473 | 1 | 5 |
| α-helix | 474-476 | 3 | |
| β-strand | 486-492 | 7 | 5 |
| β-strand | 500-506 | 7 | 6 |
| β-strand | 513-516 | 4 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| De-novo designed binder NY1-B04 | A | protein | 145 | synthetic construct | |
| HLA class I histocompatibility antigen, A alpha chain | B | protein | 276 | Homo sapiens | Q861F7 (AlphaFold model) |
| Beta-2-microglobulin | C | protein | 100 | Homo sapiens | P61769 (AlphaFold model) |
| NY-ESO-1-derived peptide SLLMWITQC | D | protein | 9 | Escherichia coli | P78358 (AlphaFold model) |
>9NNF_1 De-novo designed binder NY1-B04 (chains A) MKEELRAAAAELLAAAEALAEELRRLGLEEAAAHVLAAARHVAAALELIAATPASELNPE LKREVAAHLREAAAHFEAAAEIVAAEDPLAGAMLREAALAARSMAAYVLHSSPEEALQQA AVFATGLAGAMLTMTGLVRERLAAR
>9NNF_2 HLA class I histocompatibility antigen, A alpha chain (chains B) GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP
>9NNF_3 Beta-2-microglobulin (chains C) MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM
>9NNF_4 NY-ESO-1-derived peptide SLLMWITQC (chains D) SLLMWITQC
De novo-designed pMHC binders facilitate T cell-mediated cytotoxicity toward cancer cells. Johansen, K.H., Wolff, D.S., Scapolo, B. et al. Science (2025) 389:380-385. DOI 10.1126/science.adv0422 · PubMed
Other PDB entries of the same protein (UniProt Q861F7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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