8V50: HLA-B*35:01-NP6 with D1 TCR

Crystal structure of a HLA-B*35:01-NP6 with D1 TCR. Determined by X-ray diffraction at 2.65 Å resolution. Released 18 Dec 2024.

Method: X-ray diffraction
Resolution: 2.65 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 20
Atoms: 27,419
Mol. weight: 374.86 kDa
Released: 18 Dec 2024

Explore 8V50 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V50 contains 80 α-helices and 297 β-strands across 20 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	50-52	3
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
α-helix	182	1
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	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	253-256	4
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	44-45	2	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

Chains C, H, M and R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	8

Chain D: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	9
β-strand	10-14	5	10
β-strand	19-26	8	9
β-strand	38-44	7	10
β-strand	51-56	6	10
β-strand	64-68	5	9
β-strand	76-81	6	9
β-strand	86-91	6	9
α-helix	96-98	3
β-strand	100-107	8	10
β-strand	113-115	3	10
β-strand	119-124	6	10
β-strand	133-137	5	11
β-strand	138-139	2	12
β-strand	146-153	8	11
β-strand	168-169	2	11
α-helix	170-172	3
β-strand	173-177	5	11
β-strand	182-191	10	11
α-helix	198-201	4
β-strand	211	1	11

Chain E: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	14
β-strand	19-24	6	13
β-strand	38-44	7	14
β-strand	51-57	7	14
β-strand	64-67	4	14
β-strand	76-79	4	13
β-strand	87-91	5	13
α-helix	96-98	3
β-strand	100-107	8	14
β-strand	110	1	8
β-strand	116-117	2	14
β-strand	121-126	6	14
β-strand	133	1	15
β-strand	136-141	6	12
α-helix	142-143	2
α-helix	144-150	7
β-strand	152-162	11	12
β-strand	163	1	15
β-strand	167-173	7	16
β-strand	176-177	2	16
β-strand	182-184	3	12
α-helix	188	1
β-strand	189-190	2	12
β-strand	200-209	10	12
α-helix	210-214	5
β-strand	219-226	8	16
β-strand	229	1	17
α-helix	240-241	2
β-strand	243	1	17
β-strand	245-252	8	16

Chain F: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
α-helix	20	1
β-strand	21-28	8	18
β-strand	31-37	7	18
β-strand	46-47	2	18
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	18
α-helix	104	1
β-strand	109-118	10	18
β-strand	121-126	6	18
β-strand	133-135	3	18
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
β-strand	183	1	19
α-helix	184-185	2
β-strand	186-193	8	20
β-strand	198-208	11	20
β-strand	209	1	19
β-strand	214-219	6	21
β-strand	222-223	2	21
β-strand	228-230	3	20
α-helix	231-233	3
β-strand	234-235	2	20
β-strand	241-250	10	20
α-helix	254-256	3
β-strand	257-262	6	21
β-strand	270-272	3	21

Chain G: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	22
α-helix	4-5	2
β-strand	6-11	6	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	36-41	6	24
β-strand	45	1	24
β-strand	50-51	2	23
α-helix	52-54	3
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-83	6	24
β-strand	91-94	4	24

Chain I: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	26
β-strand	10-14	5	27
β-strand	19-26	8	26
β-strand	38-44	7	27
β-strand	51-56	6	27
β-strand	64-68	5	26
β-strand	76-81	6	26
β-strand	86-91	6	26
α-helix	96-98	3
β-strand	101-107	7	27
β-strand	113-115	3	27
β-strand	119-124	6	27
β-strand	133-137	5	28
β-strand	138-139	2	29
β-strand	146-151	6	28
α-helix	160-162	3
β-strand	168-169	2	28
α-helix	170-172	3
β-strand	173-177	5	28
β-strand	182-191	10	28
β-strand	211	1	28

9 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
HLA-B35	A, F, K, P	protein	274	Homo sapiens	O19626 (AlphaFold model)
Beta-2-microglobulin	B, G, L, Q	protein	100	Homo sapiens	P61769 (AlphaFold model)
NP6 epitope H1N1	C, H, M, R	protein	9	Influenza A virus	Q09159
D1 TCR alpha chain	D, I, N, S	protein	197	Homo sapiens
D1 TCR beta chain	E, J, O, T	protein	242	Homo sapiens

Sequence of entity 1 (A, F, K, P), FASTA

>8V50_1 HLA-B35 (chains A, F, K, P)
SHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYWD
RNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDGK
DYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQR
ADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTF
QKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, G, L, Q), FASTA

>8V50_2 Beta-2-microglobulin (chains B, G, L, Q)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H, M, R), FASTA

>8V50_3 NP6 epitope H1N1 (chains C, H, M, R)
LPFDKSTVM

Sequence of entity 4 (D, I, N, S), FASTA

>8V50_4 D1 TCR alpha chain (chains D, I, N, S)
QSLEQPSEVTAVEGAIVQINCTYQTSGFYGLSWYQQHDGGAPTFLSYNALDGLEETGRFS
SFLSRSDSYGYLLLQELQMKDSASYFCAVDTGGFKTIFGAGTRLFVKANIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTFFP

Sequence of entity 5 (E, J, O, T), FASTA

>8V50_5 D1 TCR beta chain (chains E, J, O, T)
GVSQSPRYKVAKRGQDVALRCDPISGHVSLFWYQQALGQGPEFLTYFQNEAQLDKSGLPS
DRFFAERPEGSVSTLKIQRTQQEDSAVYLCASSPTGGQETQYFGPGTRLLVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Primary citation

Molecular determinants of cross-strain influenza A virus recognition by alpha beta T cell receptors. Quinones-Parra, S.M., Gras, S., Nguyen, T.H.O. et al. Sci Immunol (2025) 10:eadn3805-eadn3805. DOI 10.1126/sciimmunol.adn3805 · PubMed

Other PDB entries of the same protein (UniProt O19626 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FYY 1.5 Å, The role of T cell receptor alpha genes in directing human MHC restriction
2CIK 1.75 Å, Insights Into Crossreactivity in Human Allorecognition: The Structure of HLA-B35011…
2FZ3 1.9 Å, The role of T cell receptor alpha genes in directing human MHC restriction
8V51 2.1 Å, Crystal structure of a HLA-B*35:01-NP10 with D1 TCR

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