9NNF: De-novo designed binder NY1-B04

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.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: synthetic construct, Homo sapiens, Escherichia coli
Chains: 4
Atoms: 4,185
Mol. weight: 59.98 kDa
Released: 23 Jul 2025

Explore 9NNF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

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.

Chain A: 5 helices, 0 β-strands

Element	Residues	Length
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

Chain B: 9 helices, 17 β-strands

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

Chain C: 1 helix, 8 β-strands

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

Molecules and chains

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)

Sequence of entity 1 (A), FASTA

>9NNF_1 De-novo designed binder NY1-B04 (chains A)
MKEELRAAAAELLAAAEALAEELRRLGLEEAAAHVLAAARHVAAALELIAATPASELNPE
LKREVAAHLREAAAHFEAAAEIVAAEDPLAGAMLREAALAARSMAAYVLHSSPEEALQQA
AVFATGLAGAMLTMTGLVRERLAAR

Sequence of entity 2 (B), FASTA

>9NNF_2 HLA class I histocompatibility antigen, A alpha chain (chains B)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 3 (C), FASTA

>9NNF_3 Beta-2-microglobulin (chains C)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 4 (D), FASTA

>9NNF_4 NY-ESO-1-derived peptide SLLMWITQC (chains D)
SLLMWITQC

Primary citation

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:

7KGQ 1.34 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N222-230
7KGP 1.4 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N316-324
7KGR 1.55 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N159-167
7KGS 1.58 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N138-146
7T5M 1.67 Å, Structure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex
7PDW 1.82 Å, Crystal structure of parent TCR (728) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer…
7KGT 1.9 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234
7SIS 1.9 Å, SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01
7PBC 2.04 Å, Crystal structure of engineered TCR (796) complexed to HLA-A*02:01 presenting MAGE-A10…
7KGO 2.15 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N351-359
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
8FJA 3.0 Å, CryoEM structure of HLA-A2 MAGEA4 (230-239) in complex with REGN6972 Fab

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