9YTF: TCR mimic antibody vAB-30

TCR mimic antibody vAB-30 in complex with MAGE-A3 in HLA-A1. Determined by electron microscopy at 2.6 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 7,270
Mol. weight: 103.4 kDa
Released: 17 Dec 2025

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

Secondary structure: helices and β-sheets

9YTF contains 24 α-helices and 87 β-strands across 5 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: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	19-20	2
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-54	5
α-helix	57-85	29
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	152-159	8
α-helix	160-164	5
α-helix	165-179	15
β-strand	183	1	2
β-strand	186	1	3
β-strand	189-193	5	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
α-helix	231-233	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	270-273	4	4

Chain B: 1 helix, 11 β-strands

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
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	8
β-strand	12-14	3	9
β-strand	19-26	8	8
α-helix	30-32	3
β-strand	35-42	8	9
β-strand	46-53	8	9
β-strand	59-61	3	9
β-strand	69-74	6	8
β-strand	79-85	7	8
α-helix	89-91	3
β-strand	93-100	8	9
β-strand	106-108	3	9
β-strand	112-116	5	9

Chain F: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	10
β-strand	10-12	3	11
β-strand	18-20	3	10
β-strand	22-25	4	10
β-strand	33-39	7	11
β-strand	45-52	8	11
β-strand	57-60	4	11
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	109-110	2	11
β-strand	114-118	5	11
α-helix	121-123	3
β-strand	124	1	12
β-strand	127-131	5	13
α-helix	135-137	3
β-strand	138-139	2	13
β-strand	142-152	11	13
β-strand	153	1	12
β-strand	158-161	4	14
α-helix	162-164	3
β-strand	166	1	14
β-strand	170-172	3	13
α-helix	173-175	3
β-strand	176-177	2	13
β-strand	183-192	10	13
α-helix	193-195	3
β-strand	202-207	6	14
β-strand	212-217	6	14

Chain G: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-13	4	16
β-strand	19-25	7	15
β-strand	33-38	6	16
β-strand	45-49	5	16
β-strand	53-54	2	16
α-helix	55	1
β-strand	62-65	4	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	85-93	9	16
β-strand	96-99	4	16
β-strand	103-107	5	16
β-strand	112	1	17
β-strand	115-119	5	18
α-helix	120-122	3
α-helix	123-128	6
β-strand	130-140	11	18
β-strand	141	1	17
β-strand	145-151	7	19
β-strand	154-155	2	19
β-strand	160-164	5	18
α-helix	165-168	4
β-strand	174-183	10	18
α-helix	184-189	6
β-strand	192-199	8	19
β-strand	206-211	6	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	275	Homo sapiens	A0A1D3TZM3 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Melanoma-associated antigen 3	C	protein	9	Homo sapiens	P43357 (AlphaFold model)
AD01-VHH	D	protein	115	Homo sapiens
vAB30 light chain	F	protein	218	synthetic construct
vAB30 heavy chain	G	protein	215	synthetic construct

Sequence of entity 1 (A), FASTA

>9YTF_1 MHC class I antigen (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYW
DQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG
KDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWP

Sequence of entity 2 (B), FASTA

>9YTF_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>9YTF_3 Melanoma-associated antigen 3 (chains C)
EVDPIGHLY

Sequence of entity 4 (D), FASTA

>9YTF_4 AD01-VHH (chains D)
EVKLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQTPGKQRDLVADISSGGSTKYG
DSVKGRFTISRDNTKNTVYLQMNSLKPEDTAVYYCYGLSYSNDDYWGQGTQVTVS

Sequence of entity 5 (F), FASTA

>9YTF_5 vAB30 light chain (chains F)
QVQLVQSGAEVKKPGSSVKVSCKASGGSIADGYISWVRQAPGQGLEWMGGILPRVQYTNY
AQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARSPTATAAALKIWGQGTMVTVSS
ASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSS
GLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKV

Sequence of entity 6 (G), FASTA

>9YTF_6 vAB30 heavy chain (chains G)
DIQMTQSPSTLSASVGDRVTITCRASRDIGRYLAWYQQKPGKAPKLLIYLSSSLESGVPS
RFSGSGSGTEFTLTISSLQPDDFATYYCQQYSIANQLTFGGGTKVEIKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Primary citation

Targeting peptide-MHC complexes with designed T cell receptors and antibodies. Motmaen, A., Jude, K.M., Wang, N. et al. bioRxiv (2025). DOI 10.1101/2025.11.19.689381 · PubMed

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