9J4U: MHC class I antigen

Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors. Determined by X-ray diffraction at 2.17 Å resolution. Released 13 Aug 2025.

Method: X-ray diffraction
Resolution: 2.17 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 5
Atoms: 6,777
Mol. weight: 95.25 kDa
Released: 13 Aug 2025

Explore 9J4U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9J4U contains 27 α-helices and 71 β-strands across 4 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	51-54	4
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	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	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
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	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
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

Chain D: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
α-helix	10	1
β-strand	11-14	4	9
β-strand	19-25	7	8
β-strand	32-38	7	9
β-strand	45-50	6	9
β-strand	54-57	4	8
β-strand	60-65	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-92	9	9
β-strand	96-99	4	9
β-strand	103-108	6	9
α-helix	109	1
β-strand	117-123	7	10
β-strand	130-135	6	10
α-helix	141-146	6
β-strand	151-153	3	10
α-helix	154-156	3
β-strand	157-161	5	10
β-strand	166-175	10	10
α-helix	182-185	4
β-strand	196	1	10

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
α-helix	25-26	2
β-strand	31-38	8	12
β-strand	42-50	9	12
β-strand	53-57	5	12
β-strand	64-68	5	11
β-strand	74-78	5	11
α-helix	83-85	3
β-strand	87-94	8	12
β-strand	103-104	2	12
β-strand	108-113	6	12
β-strand	120	1	13
α-helix	121-122	2
β-strand	123-128	6	10
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	10
β-strand	150	1	13
β-strand	154-160	7	14
β-strand	163-165	3	14
β-strand	169-171	3	10
α-helix	175	1
β-strand	176-177	2	10
β-strand	187-196	10	10
α-helix	197-201	5
β-strand	206-213	8	14
β-strand	216	1	15
β-strand	230	1	15
β-strand	232-239	8	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	276	Homo sapiens	Q8WLS4 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
LLL epitope specific TCR APHLA	D	protein	204	Homo sapiens
LLL epitope specific TCR BETA	E	protein	244	Homo sapiens
Nucleoprotein	C	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9J4U_1 MHC class I antigen (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>9J4U_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D), FASTA

>9J4U_3 LLL epitope specific TCR APHLA (chains D)
MRKEVEQDPGPFNVPEGATVAFNCTYSNSASQSFFWYRQDCRKEPKLLMSVYSSGNEDGR
FTAHVNRASQYISLLIRDSKLSDSATYLCVQGAAGNKLTFGGGTRVLVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E), FASTA

>9J4U_4 LLL epitope specific TCR BETA (chains E)
MDSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGN
ILERFSAQQFPDLHSELNLSSLELGDSALYFCASSVELNSYEQYFGPGTRLTVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Sequence of entity 5 (C), FASTA

>9J4U_5 Nucleoprotein (chains C)
LLLDRLNQL

Primary citation

Structural insights into clonal restriction and diversity in T cell recognition of two immunodominant SARS-CoV-2 nucleocapsid epitopes. Yuan, P., Chen, G., Li, Y. et al. Nat Commun (2025) 16:11457-11457. DOI 10.1038/s41467-025-66322-6 · PubMed

Other PDB entries of the same protein (UniProt Q8WLS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X7U 1.59 Å, Complex of HLA-A2, a class I MHC, with a UTP20 peptide
9WK0 1.8 Å, Neoantigen Rac1P29S-HLA-A2
21GJ 1.83 Å, Neoantigen p53Y220D-HLA-A2
21EX 2.02 Å, Wild tipe p53WT-HLA-A2
9XME 2.04 Å, Complex of HLA-A2, a class I MHC, with a wild type UTP20 peptide
9PIX 2.35 Å, Mur14 Fab with HBV c18V pMHC
9PKC 2.5 Å, Mur35 Fab with HBV c18V pMHC
9PKF 2.6 Å, Mur35 Fab with HBV c18I pMHC
9PKV 2.72 Å, HU-38 Fab with PRAME pMHC
9LLU 2.87 Å, p53 epitope specific TCR 4414A binding to p53Y220D-HLA-A2
3HG1 3.0 Å, Germline-governed recognition of a cancer epitope by an immunodominant human T cell…
9C96 3.0 Å, Cryo-EM structure of TAP binding protein related (TAPBPR) in complex with HLA-A*02:01…

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