28IL: P1-15 T-cell Receptor

P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 15 Jul 2026.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 10
Atoms: 13,408
Mol. weight: 190.61 kDa
Released: 15 Jul 2026

Explore 28IL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

28IL contains 46 α-helices and 149 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, 20 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	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
β-strand	183	1	2
α-helix	184-185	2
β-strand	189-193	5	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-246	6	3
β-strand	248-249	2	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 1 helix, 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	45	1	7
β-strand	50-51	2	6
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: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	11-14	4	9
β-strand	19-25	7	8
β-strand	32-38	7	10
β-strand	44-49	6	10
β-strand	55-57	3	8
β-strand	60-65	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	85-93	9	10
β-strand	98-102	5	10
β-strand	106-107	2	10
β-strand	108-111	4	9
β-strand	120-124	5	11
α-helix	125-127	3
β-strand	133-138	6	11
β-strand	155-156	2	11
β-strand	162-163	2	12
α-helix	165-167	3
β-strand	170-171	2	12
β-strand	173-178	6	11
β-strand	199	1	11

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	13
β-strand	13-17	5	14
β-strand	22-24	3	15
β-strand	25-28	4	13
β-strand	34-41	8	14
β-strand	45-52	8	14
β-strand	59-60	2	14
β-strand	67-70	4	15
β-strand	76	1	13
β-strand	78-81	4	15
α-helix	86-88	3
β-strand	90-97	8	14
α-helix	103-104	2
β-strand	105-106	2	14
β-strand	110-115	6	14
α-helix	118-120	3
β-strand	122	1	16
β-strand	125-129	5	17
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	17
β-strand	152	1	16
β-strand	156-162	7	18
β-strand	165-167	3	18
β-strand	171-173	3	17
β-strand	178-179	2	17
β-strand	189-198	10	17
α-helix	199-203	5
β-strand	208-215	8	18
β-strand	218	1	19
α-helix	229-230	2
β-strand	232	1	19
β-strand	234-241	8	18

Chain F: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	20
α-helix	20	1
β-strand	21-28	8	20
β-strand	31-37	7	20
α-helix	45	1
β-strand	46-47	2	20
α-helix	51-54	4
α-helix	57-84	28
β-strand	94-103	10	20
β-strand	109-118	10	20
β-strand	122-126	5	20
β-strand	133-135	3	20
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	21
β-strand	189-193	5	22
β-strand	199-208	10	22
β-strand	209	1	21
β-strand	213-219	7	23
β-strand	222-223	2	23
β-strand	228-230	3	22
β-strand	234-235	2	22
β-strand	241-249	9	22
α-helix	250	1
α-helix	254-256	3
β-strand	257-263	7	23
β-strand	270-273	4	23

Chain G: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	24
β-strand	9-11	3	25
β-strand	21-30	10	25
β-strand	31	1	24
β-strand	36-41	6	26
β-strand	45	1	26
β-strand	50-51	2	25
β-strand	55-56	2	25
β-strand	62-70	9	25
β-strand	78-83	6	26
α-helix	90	1
β-strand	91-94	4	26

Chain I: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	27
β-strand	10-14	5	28
β-strand	19-25	7	27
β-strand	32-38	7	28
β-strand	45-49	5	28
β-strand	55-57	3	27
β-strand	60-65	6	27
β-strand	70-75	6	27
α-helix	80-82	3
β-strand	85-94	10	28
β-strand	97-102	6	28
β-strand	106-111	6	28
β-strand	120-124	5	29
α-helix	125	1
β-strand	126	1	30
β-strand	134-138	5	29
β-strand	155-156	2	29
β-strand	162-164	3	31
α-helix	165-167	3
β-strand	169-171	3	31
β-strand	173-177	5	29
α-helix	185-188	4

Chain J: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	32
β-strand	13-17	5	33
β-strand	22-24	3	34
β-strand	25-28	4	32
β-strand	34-40	7	33
β-strand	46-52	7	33
β-strand	59-60	2	33
β-strand	67-70	4	34
β-strand	76	1	32
β-strand	78-81	4	34
α-helix	86-88	3
β-strand	90-97	8	33
β-strand	105-106	2	33
β-strand	110-115	6	33
α-helix	118-120	3
β-strand	122	1	35
β-strand	125-129	5	30
α-helix	130-132	3
α-helix	133-139	7
β-strand	141-151	11	30
β-strand	152	1	35
β-strand	156-162	7	36
β-strand	165-167	3	36
β-strand	171-173	3	30
α-helix	177-179	3
β-strand	189-198	10	30
α-helix	199-203	5
β-strand	208-215	8	36
β-strand	218	1	37
α-helix	229-230	2
β-strand	232	1	37
β-strand	234-241	8	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, F	protein	276	Homo sapiens	A0A411J078 (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

>28IL_1 MHC class I antigen (chains A, F)
GSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>28IL_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>28IL_3 Spike protein S1 (chains C, H)
NYNYLYRLF

Sequence of entity 4 (D, I), FASTA

>28IL_4 P1-15 T-cell Receptor Alpha Chain (chains D, I)
MRKEVEQDPGPFNVPEGATVAFNCTYSNSASQSFFWYRQDCRKEPKLLMSVYSSGNEDGR
FTAQLNRASQYISLLIRDSKLSDSATYLCVVNMLRNSGYALNFGKGTSLLVTPHIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSP

Sequence of entity 5 (E, J), FASTA

>28IL_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 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
8RJH 2.6 Å, HLA A*2402-NF9_6F pMHC complex
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

Browse structure collections

About this viewer

MolViewer shows 28IL 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.