9DY8: HLA-B*18:01

Crystal structure of HLA-B*18:01 in complex with PEMTFFSVK, an 9-mer epitope from Influenza B. Determined by X-ray diffraction at 2.0 Å resolution. Released 13 Aug 2025.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, Influenza B virus (B/Wisconsin/22/2017)
Chains: 3
Atoms: 3,382
Mol. weight: 45.34 kDa
Released: 13 Aug 2025

Explore 9DY8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DY8 contains 15 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: 13 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	50-54	5
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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
α-helix	182	1
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
α-helix	225-227	3
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	270-272	3	4

Chain B: 2 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
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	276	Homo sapiens	S6AU73 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
RNA-directed RNA polymerase catalytic subunit	C	protein	9	Influenza B virus (B/Wisconsin/22/2017)	P13871

Sequence of entity 1 (A), FASTA

>9DY8_1 MHC class I antigen (chains A)
GSHSMRYFHTSVSRPGRGEPRFISVGYVDGTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQISKTNTQTYRESLRNLRGYYNQSEAGSHTLQRMYGCDVGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGTCVEWLRRHLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>9DY8_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>9DY8_3 RNA-directed RNA polymerase catalytic subunit (chains C)
PEMTFFSVK

Primary citation

Characterisation of an influenza B virus-derived peptide presented by HLA-B*18:01. Murdolo, L.D., Liwei Leong, S., Maddumage, J.C. et al. Biochem J (2025) 482:811-820. DOI 10.1042/BCJ20240739 · PubMed

Other PDB entries of the same protein (UniProt S6AU73 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ROP 1.15 Å, Crystal structure of HLA B*18:01 in complex with QEIRTFSF, an 8-mer epitope from…
8ROO 1.4 Å, Crystal structure of HLA B*18:01 in complex with YERMCNIL, an 8-mer epitope from…
8RNG 1.45 Å, Crystal structure of HLA B*18:01 in complex with TEVETYVL, an 8-mer epitope from…
8RNH 1.6 Å, Crystal structure of HLA B*18:01 in complex with EEIEITTHF, an 9-mer epitope from…

Browse structure collections

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