9DL1: Tracer-I

Crystal Structure of HLA-A*02:01/NY-ESO-1 (SLLMWITQV) and a target specific TRACeR-I. Determined by X-ray diffraction at 2.3 Å resolution. Released 20 Nov 2024.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,899
Mol. weight: 122.49 kDa
Released: 20 Nov 2024

Explore 9DL1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DL1 contains 37 α-helices and 60 β-strands across 6 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	2-20	19
α-helix	27-29	3
α-helix	30-54	25
α-helix	65-76	12
α-helix	77-81	5
α-helix	95-118	24
α-helix	119-123	5

Chain B: 9 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	50-52	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	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	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	257-262	6	4
β-strand	270-273	4	4

Chain C: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
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

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	2-20	19
α-helix	30-53	24
α-helix	65-76	12
α-helix	77-81	5
α-helix	83-86	4
α-helix	94-122	29

Chain F: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	138-149	12
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-208	11	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
β-strand	228-230	3	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
α-helix	254-256	3
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
α-helix	46	1
β-strand	50-51	2	13
α-helix	52-54	3
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tracer-I	A, D	protein	132	Homo sapiens
MHC class I antigen, A-2 alpha chain	B, F	protein	276	Homo sapiens	A0A5B8RNS7 (AlphaFold model)
Beta-2-microglobulin	C, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Cancer/testis antigen 1	E, H	protein	9	Homo sapiens	P78358 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9DL1_1 TRACeR-I (chains A, D)
MDKEIAKEIFNMMFMLLWRVFRSQRIDANNVELIKFNIRVLDWIMAEADNDLCYFIGTHD
KCENPKEQWVANYQNLNNVVFTNKELEDIYDLSNKEETKEVLKKFKEKVNQFYRHAFDII
NKYGLEHHHHHH

Sequence of entity 2 (B, F), FASTA

>9DL1_2 MHC class I antigen, A-2 alpha chain (chains B, F)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 3 (C, G), FASTA

>9DL1_3 Beta-2-microglobulin (chains C, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 4 (E, H), FASTA

>9DL1_4 Cancer/testis antigen 1 (chains E, H)
SLLMWITQV

Primary citation

Targeting peptide antigens using a multiallelic MHC I-binding system. Du, H., Mallik, L., Hwang, D. et al. Nat Biotechnol (2025) 43:1683-1693. DOI 10.1038/s41587-024-02505-8 · PubMed

Other PDB entries of the same protein (UniProt A0A5B8RNS7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9GV7 1.86 Å, Structure of reverse docking TCR in complex with peptide-HLA
6TMO 2.1 Å, Structure determination of an enhanced affinity TCR, a24b17, in complex with HLA-A*02:01…
9SOK 2.5 Å, Structure of three-domain single chain TCR-581 in complex with Peptide-HLA
9GV6 2.77 Å, Structure of TCR in complex with peptide-HLA
9SOL 2.93 Å, Structure of TCR-581 in complex with Peptide-HLA

Browse structure collections

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