8HN4: MHC class I antigen

Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope QYIKWPWYI. Determined by X-ray diffraction at 2.85 Å resolution. Released 27 Dec 2023.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 3,156
Mol. weight: 48.61 kDa
Released: 27 Dec 2023

Explore 8HN4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HN4 contains 10 α-helices and 31 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: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	27-38	12	1
β-strand	42-52	11	1
β-strand	55-61	7	1
β-strand	70-71	2	1
α-helix	74-76	3
α-helix	81-108	28
β-strand	118-127	10	1
β-strand	133-142	10	1
β-strand	145-150	6	1
β-strand	157-159	3	1
α-helix	162-172	11
α-helix	176-182	7
α-helix	183-187	5
α-helix	188-198	11
α-helix	200-203	4
β-strand	207	1	2
α-helix	208-209	2
β-strand	210	1	3
β-strand	213-217	5	4
β-strand	222-232	11	4
β-strand	233	1	2
β-strand	238-243	6	5
β-strand	246-247	2	5
β-strand	252-254	3	4
β-strand	258-259	2	4
β-strand	265-274	10	4
β-strand	281-286	6	5
β-strand	294-296	3	5

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	308	Homo sapiens	F6IR24 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
SARS-CoV-2 T-cell epitope QYIKWPWYI	E	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8HN4_1 MHC class I antigen (chains A)
MNSVDGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQE
GPEYWDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQ
YAYDGKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENG
KETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRP
AGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPGSGLNDIFEAQKIEWHAAA
LEHHHHHH

Sequence of entity 2 (B), FASTA

>8HN4_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E), FASTA

>8HN4_3 SARS-CoV-2 T-cell epitope QYIKWPWYI (chains E)
QYIKWPWYI

Primary citation

Immune escape at SARS- CoV-2 killer T cell epitope. Deng, S.S., Jin, T.C., Xu, Z.H. To be published.

Other PDB entries of the same protein (UniProt F6IR24 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8EK5 2.11 Å, Engineered scFv 10LH bound to PHOX2B/HLA-A24:02
7SRK 2.5 Å, Single chain trimer HLA-A*24:02 (Y108C, A163C) with 8mer peptide YPPVPETF

Browse structure collections

About this viewer

MolViewer shows 8HN4 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.