8RJ5: P1-15 T-cell Receptor

P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex. Determined by X-ray diffraction at 3.02 Å resolution. Released 1 Jan 2025.

Method: X-ray diffraction
Resolution: 3.02 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 10
Atoms: 13,408
Mol. weight: 190.87 kDa
Released: 1 Jan 2025

Explore 8RJ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RJ5 contains 43 α-helices and 148 β-strands across 8 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: 12 helices, 18 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
α-helix	45	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	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
α-helix	183-185	3
β-strand	189-193	5	2
β-strand	199-208	10	2
β-strand	214-219	6	3
β-strand	222-223	2	3
β-strand	229-230	2	2
α-helix	231-233	3
β-strand	234-235	2	2
β-strand	241-246	6	2
β-strand	248-249	2	2
α-helix	254-256	3
β-strand	257-262	6	3
β-strand	270-272	3	3

Chain B: 1 helix, 11 β-strands

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

Chain D: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	7
β-strand	11-14	4	8
β-strand	19-25	7	7
β-strand	32-38	7	8
β-strand	44-49	6	8
β-strand	55-57	3	7
β-strand	60-65	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-93	10	8
β-strand	98-102	5	8
β-strand	106-111	6	8
β-strand	120-124	5	9
α-helix	125-127	3
β-strand	133-138	6	9
β-strand	155-156	2	9
β-strand	162-164	3	10
α-helix	165-167	3
β-strand	169-171	3	10
β-strand	173-178	6	9
β-strand	199	1	9

Chain E: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	11
β-strand	13-17	5	12
β-strand	22-24	3	13
β-strand	25-28	4	11
β-strand	34-40	7	12
β-strand	41	1	14
β-strand	45	1	14
β-strand	48-52	5	12
β-strand	59-60	2	12
β-strand	67-70	4	13
β-strand	76	1	11
β-strand	78-81	4	13
α-helix	86-88	3
β-strand	90-97	8	12
α-helix	103-104	2
β-strand	105-106	2	12
β-strand	110-115	6	12
α-helix	118-120	3
β-strand	122	1	15
β-strand	125-129	5	16
α-helix	133-139	7
β-strand	141-151	11	16
β-strand	152	1	15
β-strand	156-162	7	17
β-strand	165-167	3	17
β-strand	171-173	3	16
β-strand	178-179	2	16
β-strand	189-198	10	16
α-helix	199-203	5
β-strand	208-215	8	17
β-strand	218	1	18
α-helix	229-230	2
β-strand	232	1	18
β-strand	234-241	8	17

Chain F: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	19
α-helix	20	1
β-strand	21-28	8	19
β-strand	31-37	7	19
α-helix	45	1
β-strand	46-47	2	19
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	19
β-strand	109-118	10	19
β-strand	122-126	5	19
β-strand	133-135	3	19
α-helix	138-148	11
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	20
β-strand	189-193	5	21
β-strand	199-208	10	21
β-strand	209	1	20
β-strand	213-219	7	22
β-strand	222-223	2	22
β-strand	228-230	3	21
β-strand	234-235	2	21
β-strand	241-249	9	21
α-helix	250	1
α-helix	254-256	3
β-strand	257-263	7	22
β-strand	270-273	4	22

Chain G: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	23
β-strand	9-11	3	24
β-strand	21-30	10	24
β-strand	31	1	23
β-strand	36-41	6	25
β-strand	45	1	25
β-strand	50-51	2	24
β-strand	55-56	2	24
β-strand	62-70	9	24
β-strand	78-83	6	25
β-strand	91-94	4	25

Chain I: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	26
β-strand	10-14	5	27
β-strand	19-25	7	26
β-strand	32-38	7	27
β-strand	44-49	6	27
β-strand	55-57	3	26
β-strand	60-65	6	26
β-strand	70-75	6	26
α-helix	80-82	3
β-strand	85-94	10	27
β-strand	97-102	6	27
β-strand	106-111	6	27
β-strand	120-124	5	28
α-helix	125	1
β-strand	126	1	29
β-strand	134-138	5	28
β-strand	155-156	2	28
β-strand	162-164	3	30
α-helix	165-167	3
β-strand	169-171	3	30
β-strand	173-177	5	28
α-helix	185-188	4

Chain J: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	31
β-strand	13-17	5	32
β-strand	22-24	3	33
β-strand	25-28	4	31
β-strand	34-40	7	32
β-strand	46-52	7	32
β-strand	59-60	2	32
β-strand	67-70	4	33
β-strand	76	1	31
β-strand	78-81	4	33
α-helix	86-88	3
β-strand	90-97	8	32
β-strand	105-106	2	32
β-strand	110-115	6	32
α-helix	118-120	3
β-strand	122	1	34
β-strand	125-129	5	29
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	29
β-strand	152	1	34
β-strand	156-162	7	35
β-strand	165-167	3	35
β-strand	171-173	3	29
β-strand	189-198	10	29
α-helix	199-203	5
β-strand	208-215	8	35
β-strand	218	1	36
α-helix	229-230	2
β-strand	232	1	36
β-strand	234-241	8	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, F	protein	277	Homo sapiens	A0A5H2UYS3 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Spike protein S1	C, H	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
P1-15 T-cell Receptor Alpha Chain	D, I	protein	204	Homo sapiens
P1-15 T-cell Receptor Beta Chain	E, J	protein	245	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>8RJ5_1 MHC class I antigen (chains A, F)
MGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETL
QRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>8RJ5_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>8RJ5_3 Spike protein S1 (chains C, H)
NYNYLYRLF

Sequence of entity 4 (D, I), FASTA

>8RJ5_4 P1-15 T-cell Receptor Alpha Chain (chains D, I)
MRKEVEQDPGPFNVPEGATVAFNCTYSNSASQSFFWYRQDCRKEPKLLMSVYSSGNEDGR
FTAQLNRASQYISLLIRDSKLSDSATYLCVVNMLRNSGYALNFGKGTSLLVTPHIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSP

Sequence of entity 5 (E, J), FASTA

>8RJ5_5 P1-15 T-cell Receptor Beta Chain (chains E, J)
GSMNAGVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDK
GEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSESGGYEQYFGPGTRLTVTEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

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 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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