9MIN: Designed minibinder to NYESO1-A*02:01

Structure of a designed minibinder to NYESO1-A*02:01. Determined by X-ray diffraction at 2.05 Å resolution. Released 6 Aug 2025.

Method: X-ray diffraction
Resolution: 2.05 Å
Organisms: Homo sapiens, synthetic construct, Lama glama
Chains: 10
Atoms: 10,482
Mol. weight: 148.05 kDa
Released: 6 Aug 2025

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

Secondary structure: helices and β-sheets

9MIN contains 43 α-helices and 84 β-strands across 8 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
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	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
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	213-219	7	4
β-strand	222-223	2	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-263	7	4
β-strand	270-272	3	4

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	19	1	7
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	8
β-strand	91-94	4	8
α-helix	95-96	2

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	3-31	29
α-helix	35-62	28
α-helix	66-91	26
α-helix	95-127	33

Chain E: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	9
β-strand	12-14	3	10
β-strand	20-27	8	9
β-strand	33-41	9	10
α-helix	46-47	2
β-strand	48-53	6	10
β-strand	59-61	3	10
β-strand	69-74	6	9
α-helix	75-77	3
β-strand	79-84	6	9
α-helix	89-91	3
β-strand	93-101	9	10
β-strand	106-108	3	10
β-strand	112-116	5	10

Chain F: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	11
α-helix	20	1
β-strand	21-28	8	11
β-strand	31-37	7	11
β-strand	46-47	2	11
α-helix	52-54	3
α-helix	57-84	28
β-strand	94-103	10	11
β-strand	109-118	10	11
β-strand	121-126	6	11
β-strand	133-135	3	11
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	12
α-helix	184-185	2
β-strand	186-192	7	13
β-strand	198-208	11	13
β-strand	209	1	12
β-strand	214-219	6	14
β-strand	222-224	3	14
β-strand	228-230	3	13
α-helix	231-233	3
β-strand	234-235	2	13
β-strand	241-250	10	13
α-helix	254-256	3
β-strand	257-262	6	14
β-strand	270-273	4	14

Chain G: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	15
α-helix	4-5	2
β-strand	6-11	6	16
β-strand	19	1	9
β-strand	21-30	10	16
β-strand	31	1	15
β-strand	36-41	6	17
β-strand	44-45	2	17
α-helix	46	1
β-strand	50-51	2	16
α-helix	52-54	3
β-strand	55-56	2	16
β-strand	62-70	9	16
β-strand	78-83	6	17
β-strand	91-94	4	17

Chain I: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	3-32	30
α-helix	35-62	28
α-helix	66-91	26
α-helix	95-126	32

Chain J: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	7
β-strand	12-14	3	18
β-strand	20-27	8	7
β-strand	33-41	9	18
α-helix	46-47	2
β-strand	48-53	6	18
β-strand	59-61	3	18
α-helix	63-65	3
β-strand	69-74	6	7
α-helix	75-77	3
β-strand	79-84	6	7
α-helix	89-91	3
β-strand	93-101	9	18
β-strand	106-108	3	18
β-strand	112-116	5	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I antigen	A, F	protein	278	Homo sapiens	Q53Z42 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	101	Homo sapiens	P61769 (AlphaFold model)
Cancer/testis antigen 1	C, H	protein	9	Homo sapiens	P78358 (AlphaFold model)
designed minibinder KH46	D, I	protein	136	synthetic construct
nanobody AD01	E, J	protein	119	Lama glama

Sequence of entity 1 (A, F), FASTA

>9MIN_1 HLA class I antigen (chains A, F)
MGGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPE
YWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAY
DGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKET
LQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGD
GTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>9MIN_2 Beta-2-microglobulin (chains B, G)
MGIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSK
DWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>9MIN_3 Cancer/testis antigen 1 (chains C, H)
SLLMWITQV

Sequence of entity 4 (D, I), FASTA

>9MIN_4 designed minibinder KH46 (chains D, I)
MGAAERLQKMLEEAKELLKKSKEYLEKAKKLLKEGKVDEALKELEKALLYLVEAVNLLRV
VSAELGDAELKALVEEAEKYLNKAVTYYYKAKLTKDPEEKKKYVEKSIEYAEKALKIAEE
AVKLAEKVVAAAAALE

Sequence of entity 5 (E, J), FASTA

>9MIN_5 nanobody AD01 (chains E, J)
EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYG
DSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVSSGAP

Primary citation

De novo design and structure of a peptide-centric TCR mimic binding module. Householder, K.D., Xiang, X., Jude, K.M. et al. Science (2025) 389:375-379. DOI 10.1126/science.adv3813 · PubMed

Other PDB entries of the same protein (UniProt Q53Z42 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TRN 1.35 Å, Crystal structure of HLA A2*01-AVYDGREHTV
8FU4 1.6 Å, HCMV US11 peptide binding to HLA-A*02:01
7UM2 1.63 Å, SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by…
7U1R 1.8 Å, SARS-CoV-2 Spike-derived peptide S1185-1193 K1191N mutant (RLNEVANNL) presented by…
8RBV 1.8 Å, SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by…
22EE 1.99 Å, Structure of HLA-A2:01 with 9-mer peptide PGS
7RTD 2.05 Å, SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01
7UR1 2.17 Å, SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01
7RTR 2.6 Å, YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL)…
8TBV 2.64 Å, Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL
6TRO 3.0 Å, Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV
9VSO 3.03 Å, Crystal structure of Fab bound to the WT1-derived RMF peptide presented by HLA-A*02:01

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