8RJH: HLA A*2402-NF9_6F pMHC complex

HLA A*2402-NF9_6F pMHC complex. Determined by X-ray diffraction at 2.6 Å resolution. Released 1 Jan 2025.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 18
Atoms: 19,159
Mol. weight: 269.45 kDa
Released: 1 Jan 2025

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

Secondary structure: helices and β-sheets

8RJH contains 70 α-helices and 180 β-strands across 12 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, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	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

Chains B, E, H, K, N and Q: 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

Chains D, G, M and P: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-54	5
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	152-161	10
α-helix	163-174	12
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	222-223	2	11
α-helix	225-227	3
β-strand	229-230	2	10
α-helix	231-233	3
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	270-273	4	11

Chain J: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	22
β-strand	21-28	8	22
β-strand	31-37	7	22
β-strand	46-47	2	22
α-helix	50-54	5
α-helix	57-84	28
β-strand	94-103	10	22
β-strand	109-118	10	22
β-strand	121-126	6	22
β-strand	133-135	3	22
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	23
β-strand	186-193	8	24
β-strand	198-208	11	24
β-strand	209	1	23
β-strand	214-219	6	25
β-strand	222-223	2	25
α-helix	225-227	3
β-strand	229-230	2	24
β-strand	234-235	2	24
β-strand	241-250	10	24
α-helix	254-256	3
β-strand	257-262	6	25
β-strand	270-273	4	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, D, G, J, M, P	protein	276	Homo sapiens	A0A411J078 (AlphaFold model)
Beta-2-microglobulin	B, E, H, K, N, Q	protein	100	Homo sapiens	P61769 (AlphaFold model)
Asn-tyr-asn-tyr-leu-phe-arg-leu-phe	C, F, I, L, O, R	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

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

>8RJH_1 MHC class I antigen (chains A, D, G, J, M, P)
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

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

>8RJH_2 Beta-2-microglobulin (chains B, E, H, K, N, Q)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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

>8RJH_3 ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE (chains C, F, I, L, O, R)
NYNYLFRLF

Primary citation

Position-5-driven reorientation of an immunodominant HLA-A*24:02 SARS-CoV-2 epitope drives universal T cell escape. Nakama, T., Wall, A., Dolton, G. et al. JCI Insight (2026) 11. DOI 10.1172/jci.insight.202235 · PubMed

Other PDB entries of the same protein (UniProt A0A411J078 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BL5 2.0 Å, KIR3DL1*001 in complex with HLA-A*24:02 presenting the TW9 peptide
8RJI 2.3 Å, HLA A*2402-NF9_5R pMHC complex
9BL6 2.4 Å, KIR3DL1*114 in complex with HLA-A*24:02 presenting the TW9 peptide
9BL9 2.6 Å, KIR3DL1*114 in complex with HLA-A*24:02 presenting the NEF peptide
9BLA 3.0 Å, KIR3DL1*086 in complex with HLA-A*24:02 presenting the NEF peptide
28IL 3.1 Å, P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex

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