7JYU: HLA-A*2402

Crystal Structure of HLA-A*2402 in complex with IYFSPIRVTF, an 10-mer epitope from Influenza B virus. Determined by X-ray diffraction at 2.75 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 6
Atoms: 6,387
Mol. weight: 90.17 kDa
Ligands: MG
Released: 14 Apr 2021

Explore 7JYU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JYU contains 29 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: 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	57-84	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	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	213-219	7	4
β-strand	222-224	3	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	253-256	4
β-strand	257-263	7	4
β-strand	270-272	3	4

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-11	6	6
α-helix	14-15	2
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
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	7
β-strand	91-94	4	7

Chains C and F: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4

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
β-strand	46-47	2	8
α-helix	50-52	3
α-helix	57-85	29
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	139-150	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	9
α-helix	184-185	2
β-strand	188-193	6	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	229-230	2	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain E: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
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
α-helix	95	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, D	protein	278	Homo sapiens	A0A5H2UYS3 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Homo sapiens	P61769 (AlphaFold model)
NP-164-173 peptide from influenza B, IYFSPIRVTF	C, F	protein	10	Influenza A virus	C0RVT5

Sequence of entity 1 (A, D), FASTA

>7JYU_1 MHC class I antigen (chains A, D)
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 2 (B, E), FASTA

>7JYU_2 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>7JYU_3 NP-164-173 peptide from influenza B, IYFSPIRVTF (chains C, F)
IYFSPIRVTF

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

CD8 + T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph. Hensen, L., Illing, P.T., Bridie Clemens, E. et al. Nat Commun (2021) 12:2931-2931. DOI 10.1038/s41467-021-23212-x · 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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