8V51: HLA-B*35:01-NP10 with D1 TCR

Crystal structure of a HLA-B*35:01-NP10 with D1 TCR. Determined by X-ray diffraction at 2.1 Å resolution. Released 18 Dec 2024.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 5
Atoms: 7,107
Mol. weight: 93.89 kDa
Ligands: PO4
Released: 18 Dec 2024

Explore 8V51 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8V51 contains 21 α-helices and 74 β-strands across 5 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: 9 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
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
β-strand	183	1	2
α-helix	184-185	2
β-strand	188-190	3	3
β-strand	200-208	9	3
β-strand	209	1	2
β-strand	216-217	2	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-248	8	3
α-helix	254-256	3
β-strand	259-260	2	4
β-strand	271-272	2	4

Chain B: 2 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	22-30	9	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-69	8	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	7	1	8

Chain D: 5 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
α-helix	116	1
β-strand	119-124	6	10
α-helix	125	1
β-strand	133-137	5	11
β-strand	138	1	12
β-strand	146-151	6	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	212	1	11

Chain E: 5 helices, 26 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	136-140	5	16
β-strand	141	1	12
α-helix	142-143	2
α-helix	144-150	7
β-strand	152-162	11	16
β-strand	163	1	15
β-strand	167-173	7	17
β-strand	176-178	3	17
β-strand	182-184	3	16
β-strand	189-190	2	16
β-strand	200-209	10	16
α-helix	210-214	5
β-strand	219-226	8	17
β-strand	229	1	18
α-helix	240-241	2
β-strand	243	1	18
β-strand	245-252	8	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA-B35	A	protein	273	Homo sapiens	O19626 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
Leu-pro-phe-glu-lys-ser-thr-val-met	C	protein	9	Influenza A virus
D1 TCR alpha chain	D	protein	198	Homo sapiens
D1 TCR beta chain	E	protein	242	Homo sapiens

Sequence of entity 1 (A), FASTA

>8V51_1 HLA-B35 (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLR

Sequence of entity 2 (B), FASTA

>8V51_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEADEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>8V51_3 LEU-PRO-PHE-GLU-LYS-SER-THR-VAL-MET (chains C)
LPFEKSTVM

Sequence of entity 4 (D), FASTA

>8V51_4 D1 TCR alpha chain (chains D)
QSLEQPSEVTAVEGAIVQINCTYQTSGFYGLSWYQQHDGGAPTFLSYNALDGLEETGRFS
SFLSRSDSYGYLLLQELQMKDSASYFCAVDTGGFKTIFGAGTRLFVKANIQNPDPAVYQL
RDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFA
CANAFNNSIIPEDTFFAA

Sequence of entity 5 (E), FASTA

>8V51_5 D1 TCR beta chain (chains E)
GVSQSPRYKVAKRGQDVALRCDPISGHVSLFWYQQALGQGPEFLTYFQNEAQLDKSGLPS
DRFFAERPEGSVSTLKIQRTQQEDSAVYLCASSPTGGQETQYFGPGTRLLVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	5

Water and common crystallization additives (EDO, NA) are not listed.

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
8V50 2.65 Å, Crystal structure of a HLA-B*35:01-NP6 with D1 TCR

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