8SBK: HLA-A*24:02

Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI (ATG2A). Determined by X-ray diffraction at 1.8 Å resolution. Released 6 Dec 2023.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,571
Mol. weight: 45.84 kDa
Released: 6 Dec 2023

Explore 8SBK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8SBK contains 14 α-helices and 30 β-strands across 2 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: 11 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	57-85	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	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-195	10	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	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	257-262	6	4
β-strand	270-273	4	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
α-helix	47	1
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	283	Homo sapiens	A0A5H2UYS3 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Leu-tyr-leu-pro-val-arg-val-leu-ile	C	protein	9	Homo sapiens	Q2TAZ0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8SBK_1 MHC class I antigen (chains A)
MASGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGP
EYWDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYA
YDGKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKE
TLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAG
DGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSSQP

Sequence of entity 2 (B), FASTA

>8SBK_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>8SBK_3 LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE (chains C)
LYLPVRVLI

Primary citation

Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion. Sun, Y., Florio, T.J., Gupta, S. et al. Sci Immunol (2023) 8:eadj5792-eadj5792. DOI 10.1126/sciimmunol.adj5792 · PubMed

Other PDB entries of the same protein (UniProt A0A5H2UYS3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7JYV 1.51 Å, Crystal Structure of HLA A*2402 in complex with YFSPIRVTF, an 9-mer influenza epitope
7MJA 1.69 Å, HLA-A*24:02 bound to Neuroblastoma derived PHOX2B peptide
7EJM 1.71 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
7WT3 1.89 Å, Crystal structure of HLA-A*2402 complexed with 4-mer lipopeptide
7EJL 1.89 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-2) spike protein
7WT4 1.89 Å, Crystal structure of HLA-A*2402 complexed with 8-mer Influenza PB1 peptide
7K81 2.0 Å, KIR3DL1*005 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide
7EJN 2.11 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-HKU1) spike protein
6XQA 2.16 Å, Crystal Structure of HLA A*2402 in complex with TYQWVLKNL, an 9-mer epitope from…
7NME 2.2 Å, Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR
7NMD 2.25 Å, Human Major Histocompatibility Complex A24 Allele presenting QLPRLFPLL
7K80 2.4 Å, KIR3DL1*001 in complex with HLA-A*24:02 presenting the RYPLTFGW peptide

Browse structure collections

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