8T7R: Human leukocyte antigen A*0101

Crystal structure of human leukocyte antigen A*0101 in complex with the Fab of alloreactive antibody E07. Determined by X-ray diffraction at 3.84 Å resolution. Released 25 Dec 2024.

Method: X-ray diffraction
Resolution: 3.84 Å
Organisms: Homo sapiens, Cytomegalovirus
Chains: 50
Atoms: 63,611
Mol. weight: 972.58 kDa
Released: 25 Dec 2024

Explore 8T7R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T7R contains 268 α-helices and 779 β-strands across 41 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	54
α-helix	20	1
β-strand	21-28	8	54
β-strand	31-37	7	54
β-strand	46-47	2	54
α-helix	57-84	28
β-strand	94-102	9	54
β-strand	111-118	8	54
β-strand	121-126	6	54
β-strand	133-135	3	54
α-helix	139-147	9
α-helix	152-159	8
α-helix	160-164	5
α-helix	165-174	10
α-helix	176-179	4

Chain A: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	1
β-strand	9-12	4	2
β-strand	18-24	7	1
α-helix	27-29	3
β-strand	33-37	5	2
β-strand	44-47	4	2
β-strand	48	1	3
β-strand	52	1	3
β-strand	61-62	2	1
β-strand	65-66	2	1
β-strand	69-74	6	1
α-helix	79-81	3
β-strand	84-91	8	2
β-strand	96-99	4	2
β-strand	103-107	5	2
β-strand	113	1	4
α-helix	114-115	2
β-strand	116-120	5	5
α-helix	121-123	3
α-helix	124-127	4
β-strand	132-141	10	5
β-strand	142	1	4
β-strand	147-152	6	6
β-strand	156	1	6
β-strand	161-163	3	5
α-helix	164-166	3
β-strand	167-168	2	5
β-strand	174-182	9	5
α-helix	184-189	6
β-strand	193-199	7	6
β-strand	202-205	4	6

Chains b and P: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	59
α-helix	4-5	2
β-strand	6-11	6	60
β-strand	21-30	10	60
β-strand	31	1	59
β-strand	35-41	7	61
β-strand	44-46	3	61
β-strand	50-51	2	60
β-strand	55-56	2	60
β-strand	62-70	9	60
β-strand	78-84	7	61
β-strand	91-94	4	61
α-helix	95-96	2

Chain B: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	12
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	32-39	8	13
β-strand	46-51	6	13
β-strand	59-60	2	13
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-102	11	13
β-strand	111-114	4	13
β-strand	118-122	5	13
β-strand	128	1	14
α-helix	129-130	2
β-strand	131-135	5	15
α-helix	136-138	3
β-strand	146-156	11	15
β-strand	157	1	14
β-strand	162-165	4	16
α-helix	166-168	3
β-strand	170	1	16
β-strand	174-176	3	15
α-helix	177-179	3
β-strand	180-181	2	15
β-strand	187-196	10	15
α-helix	199-202	4
β-strand	206-211	6	16
β-strand	216-221	6	16

Chain c: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	65
β-strand	9-12	4	66
β-strand	18-23	6	65
α-helix	27-29	3
β-strand	33-37	5	66
β-strand	44-47	4	66
β-strand	48	1	67
β-strand	52	1	67
β-strand	61-62	2	65
β-strand	65-66	2	65
β-strand	69-74	6	65
α-helix	79-81	3
β-strand	83-91	9	66
β-strand	96-99	4	66
β-strand	103-107	5	66
β-strand	113	1	68
α-helix	114-115	2
β-strand	116-120	5	69
α-helix	121-123	3
α-helix	124-127	4
β-strand	132-141	10	69
β-strand	142	1	68
β-strand	147-152	6	70
β-strand	156	1	70
β-strand	161-163	3	69
α-helix	164-166	3
β-strand	167-168	2	69
β-strand	174-182	9	69
α-helix	184-189	6
β-strand	193-199	7	70
β-strand	202-204	3	70

Chain C: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	22
α-helix	13-14	2
β-strand	21-28	8	22
β-strand	31-37	7	22
β-strand	46-47	2	22
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	152-158	7
α-helix	159-164	6
α-helix	165-174	10
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
β-strand	228-230	3	24
α-helix	231-233	3
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	270-272	3	25

Chain d: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	77
β-strand	10-12	3	78
β-strand	18-25	8	77
α-helix	29-31	3
β-strand	32-39	8	78
β-strand	46-51	6	78
β-strand	59-60	2	78
α-helix	62-64	3
β-strand	68-73	6	77
β-strand	78-83	6	77
α-helix	88-90	3
β-strand	92-102	11	78
β-strand	111-114	4	78
β-strand	118-122	5	78
β-strand	128	1	79
α-helix	129-130	2
β-strand	131-135	5	80
α-helix	136-138	3
β-strand	148-156	9	80
β-strand	157	1	79
β-strand	162-165	4	81
β-strand	170	1	81
β-strand	174-176	3	80
α-helix	177-179	3
β-strand	180-181	2	80
β-strand	187-194	8	80
β-strand	206-211	6	81
α-helix	212-214	3
β-strand	216-221	6	81

Chains D, f, H and T: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	29
α-helix	4-5	2
β-strand	6-11	6	30
β-strand	21-30	10	30
β-strand	31	1	29
β-strand	36-41	6	31
β-strand	44-45	2	31
α-helix	46	1
β-strand	50-51	2	30
β-strand	55-56	2	30
β-strand	62-70	9	30
β-strand	78-83	6	31
β-strand	91-94	4	31
α-helix	95-96	2

25 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Light chain from antibody JTK191b E07	A, E, I, M, Q, U, Y, c, g, k, o, s	protein	214	Homo sapiens
Fab heavy chain from antibody JTK191b E07	B, F, J, N, R, V, Z, d, h, l, p, t	protein	240	Homo sapiens
MHC class I antigen (Fragment)	C, G, K, O, S, W, a, e, i	protein	274	Homo sapiens	F6IQR9 (AlphaFold model)
peptide	0, 1, 2, 3, 4, 5, 6, 7, 8	protein	9	Cytomegalovirus	P16790
Beta-2-microglobulin	D, H, L, P, T, X, b, f	protein	99	Homo sapiens	P61769 (AlphaFold model)

Sequence of entity 1 (A, E, I, M, Q, U, Y, c, g, k, o, s), FASTA

>8T7R_1 Light chain from antibody JTK191b E07 (chains A, E, I, M, Q, U, Y, c, g, k, o, s)
QSVSTQPPSVSVAPGQTARITCGGNNIGSKSVHWYRQKPGQAPVLVVYDNNARPSGIPER
ISGSNFANTATLTISRVEAGDEADYYCHVWDSSSDHVVFGGGTKLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 2 (B, F, J, N, R, V, Z, d, h, l, p, t), FASTA

>8T7R_2 Fab heavy chain from antibody JTK191b E07 (chains B, F, J, N, R, V, Z, d, h, l, p, t)
QVQLQESGGGVVQPGGSLRLSCAASGFNFSNYGMHWVRQTPGKGLEWVASIPYDGSHQWH
ADSVKGRFTISRDNSKNTLYLQINSLRPEDTAMYYCSKARISYLSAPAWWFDPWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHTDYKDDDDK

Sequence of entity 3 (C, G, K, O, S, W, a, e, i), FASTA

>8T7R_3 MHC class I antigen (Fragment) (chains C, G, K, O, S, W, a, e, i)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQKMEPRAPWIEQEGPEYW
DQETRNMKAHSQTDRANLGTLRGYYNQSEDGSHTIQIMYGCDVGPDGRFLRGYRQDAYDG
KDYIALNEDLRSWTAADMAAQITKRKWEAVHAAEQRRVYLEGRCVDGLRRYLENGKETLQ
RTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 4 (0, 1, 2, 3, 4, 5, 6, 7, 8), FASTA

>8T7R_4 peptide (chains 0, 1, 2, 3, 4, 5, 6, 7, 8)
VTEHDTLLY

Sequence of entity 5 (D, H, L, P, T, X, b, f), FASTA

>8T7R_5 Beta-2-microglobulin (chains D, H, L, P, T, X, b, f)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Primary citation

Topography of the HLA-A protein enforces shared and convergent immunodominant B cell and antibody alloresponses in transplant recipients. Killian Jr., J.T., King, R.G., Lucander, A.C.K. et al. Immunity (2025) 58:3040-3060.e12. DOI 10.1016/j.immuni.2025.10.014 · PubMed

Other PDB entries of the same protein (UniProt F6IQR9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YIV 2.1 Å, N17.1.2 recognition of NRAS neoantigens
8YJ2 2.26 Å, N17.1.2 recognition of NRAS neoantigens
9RU5 3.26 Å, Cryo-EM structure of TCRpub/pMHC

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