8SBL: HLA-A*24:02

Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI. Determined by X-ray diffraction at 3.0 Å resolution. Released 6 Dec 2023.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 12
Atoms: 12,604
Mol. weight: 181.73 kDa
Released: 6 Dec 2023

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

Secondary structure: helices and β-sheets

8SBL contains 43 α-helices and 122 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	50-53	4
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	139-149	11
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
β-strand	183	1	2
α-helix	184-185	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	228-230	3	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
α-helix	269	1
β-strand	270-272	3	4

Chain B: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
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
β-strand	51-52	2	6
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7
α-helix	96-97	2

Chain D: 10 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
α-helix	45	1
β-strand	46-47	2	8
α-helix	50-53	4
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	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	9
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	223-224	2	11
β-strand	228-230	3	10
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 E: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
α-helix	5-6	2
β-strand	7-12	6	13
β-strand	22-31	10	13
β-strand	32	1	12
β-strand	37-42	6	14
β-strand	45-46	2	14
β-strand	51-52	2	13
β-strand	56-57	2	13
β-strand	63-71	9	13
β-strand	79-84	6	14
β-strand	92-95	4	14

Chain G: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	15
β-strand	15	1	16
β-strand	17	1	16
α-helix	20	1
β-strand	21-28	8	15
β-strand	31-37	7	15
α-helix	45	1
β-strand	46-47	2	15
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	15
β-strand	109-118	10	15
β-strand	121-126	6	15
β-strand	133-135	3	15
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
β-strand	183	1	17
β-strand	186-192	7	18
β-strand	198-208	11	18
β-strand	209	1	17
β-strand	213-219	7	19
β-strand	222-223	2	19
β-strand	228-230	3	18
β-strand	234-235	2	18
β-strand	241-250	10	18
α-helix	254-256	3
β-strand	257-263	7	19
β-strand	272	1	19

Chain H: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	20
β-strand	7-12	6	21
β-strand	22-31	10	21
β-strand	32	1	20
β-strand	37-42	6	22
β-strand	45-46	2	22
α-helix	47	1
β-strand	51-52	2	21
β-strand	56-57	2	21
β-strand	63-71	9	21
β-strand	79-84	6	22
β-strand	92-95	4	22

Chain J: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	23
β-strand	18-28	11	23
β-strand	31-37	7	23
β-strand	46-47	2	23
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-103	10	23
β-strand	109-118	10	23
β-strand	121-126	6	23
β-strand	133-135	3	23
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	24
α-helix	184-185	2
β-strand	186-193	8	25
β-strand	198-208	11	25
β-strand	209	1	24
β-strand	214-219	6	26
β-strand	222	1	26
β-strand	228-230	3	25
β-strand	234	1	25
β-strand	241-250	10	25
α-helix	254-256	3
β-strand	257-262	6	26
β-strand	270-273	4	26

Chain K: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	27
β-strand	7-12	6	28
β-strand	22-31	10	28
β-strand	32	1	27
β-strand	36-42	7	29
β-strand	45-46	2	29
α-helix	47	1
β-strand	51-52	2	28
β-strand	56-57	2	28
β-strand	63-71	9	28
β-strand	79-85	7	29
β-strand	92-95	4	29
α-helix	96-97	2

Molecules and chains

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

Sequence of entity 1 (A, D, G, J), FASTA

>8SBL_1 MHC class I antigen (chains A, D, G, J)
MASGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGP
EYWDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYA
YDGKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKE
TLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAG
DGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSSQP

Sequence of entity 2 (B, E, H, K), FASTA

>8SBL_2 Beta-2-microglobulin (chains B, E, H, K)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F, I, L), FASTA

>8SBL_3 LEU-TYR-LEU-PRO-VAL-ARG-VAL-LEU-ILE (chains C, F, I, L)
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
8SBK 1.8 Å, Structure of HLA-A*24:02 in complex with peptide, LYLPVRVLI (ATG2A).
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

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