9DIO: Hemagglutinin HA1

Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus A/Texas/37/2024 (H5N1) with LSTc. Determined by X-ray diffraction at 2.7 Å resolution. Released 4 Dec 2024.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Influenza A virus
Chains: 18
Atoms: 36,829
Mol. weight: 524.09 kDa
Ligands: NAG
Released: 4 Dec 2024

Explore 9DIO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DIO contains 127 α-helices and 430 β-strands across 18 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: 10 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	1
β-strand	18	1	2
β-strand	25-26	2	3
β-strand	34-35	2	3
β-strand	36	1	4
β-strand	39-41	3	5
β-strand	43-44	2	6
β-strand	51-54	4	7
β-strand	56	1	7
β-strand	59-60	2	8
β-strand	64	1	9
α-helix	66-71	6
β-strand	84	1	10
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	100-102	3	11
α-helix	105-111	7
β-strand	115	1	10
β-strand	117-122	6	11
α-helix	125A-126	3
β-strand	131	1	12
β-strand	136-140	5	13
β-strand	145-146	2	13
β-strand	151-153	3	11
β-strand	155	1	12
β-strand	157	1	14
β-strand	160	1	14
α-helix	162-163	2
β-strand	164-169	6	15
β-strand	175-184	10	11
α-helix	185	1
α-helix	188-195	8
β-strand	202-205	4	15
β-strand	210-213	4	15
β-strand	223	1	16
β-strand	226	1	16
β-strand	229-237	9	11
β-strand	242-247	6	15
β-strand	251-254	4	11
β-strand	256-260A	6	11
β-strand	267-269	3	8
α-helix	272-273	2
β-strand	274-279	6	7
β-strand	281-283	3	17
β-strand	286-287	2	17
β-strand	294-295	2	6
β-strand	302-304	3	17
α-helix	306	1
β-strand	307-308	2	6
β-strand	315-317	3	5
α-helix	320	1
β-strand	321	1	4
α-helix	322	1

Chain B: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-57	20
β-strand	63-65	3	17
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	160-162	3
α-helix	163-172	10

Chain C: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	18
β-strand	18	1	19
β-strand	25-26	2	20
β-strand	34-35	2	20
β-strand	36	1	21
β-strand	39-41	3	22
β-strand	43-44	2	23
β-strand	51-54	4	24
β-strand	56	1	24
β-strand	59-61	3	25
β-strand	64	1	26
α-helix	66-71	6
α-helix	77-78	2
β-strand	84	1	27
β-strand	87-89	3	25
β-strand	95	1	26
β-strand	100-102	3	28
α-helix	105-111	7
β-strand	115	1	27
β-strand	117-122	6	28
α-helix	125A-126	3
β-strand	130-131	2	29
β-strand	136-141	6	30
β-strand	144-146	3	30
β-strand	151-153	3	28
β-strand	155-156	2	29
β-strand	157	1	31
β-strand	160	1	31
α-helix	162-163	2
β-strand	164-169	6	32
β-strand	175-184	10	28
α-helix	188-195	8
β-strand	202-205	4	32
β-strand	210-213	4	32
β-strand	223	1	33
β-strand	226	1	33
β-strand	229-237	9	28
β-strand	242-247	6	32
β-strand	251-254	4	28
β-strand	256-260A	6	28
β-strand	267-269	3	25
α-helix	272-273	2
β-strand	274-279	6	24
β-strand	281-283	3	34
β-strand	286-288	3	34
β-strand	294-295	2	23
β-strand	302-304	3	34
α-helix	306	1
β-strand	307-308	2	23
β-strand	315-317	3	22
β-strand	321	1	21

Chain D: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	19
β-strand	22-28	7	18
β-strand	31-36	6	18
α-helix	38-57	20
β-strand	63-65	3	34
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	18
β-strand	137-140	4	18
α-helix	146-154	9
α-helix	160-167	8

Chain E: 10 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	35
β-strand	18	1	36
β-strand	25-26	2	37
β-strand	34-35	2	37
β-strand	36	1	38
β-strand	39-41	3	39
β-strand	43-44	2	40
β-strand	51-54	4	41
β-strand	56	1	41
β-strand	59-60	2	42
β-strand	64	1	43
α-helix	66-71	6
β-strand	84	1	44
β-strand	87-89	3	42
β-strand	95	1	43
β-strand	100-102	3	45
α-helix	105-111	7
β-strand	115	1	44
β-strand	117-122	6	45
α-helix	125A-126	3
β-strand	130-131	2	46
β-strand	136-141	6	47
β-strand	144-146	3	47
β-strand	151-153	3	45
β-strand	155-156	2	46
α-helix	162-163	2
β-strand	164-169	6	48
β-strand	175-184	10	45
α-helix	185	1
α-helix	188-195	8
β-strand	202-205	4	48
β-strand	210-213	4	48
β-strand	223	1	49
β-strand	226	1	49
β-strand	229-237	9	45
β-strand	242-247	6	48
β-strand	251-254	4	45
β-strand	256-260A	6	45
β-strand	267-269	3	42
α-helix	272-273	2
β-strand	274-279	6	41
β-strand	281-282	2	50
β-strand	294-295	2	40
β-strand	302-304	3	50
α-helix	306	1
β-strand	307-308	2	40
β-strand	315-317	3	39
α-helix	320	1
β-strand	321	1	38
α-helix	322	1

Chain F: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	36
β-strand	22-27	6	35
β-strand	32-36	5	35
α-helix	38-57	20
β-strand	63-65	3	50
α-helix	75-126	52
β-strand	130-132	3	35
β-strand	137-140	4	35
α-helix	146-154	9
α-helix	160-162	3
α-helix	163-173	11

Chain G: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	51
β-strand	18	1	52
β-strand	25-26	2	53
β-strand	34-35	2	53
β-strand	36	1	54
β-strand	39-41	3	55
β-strand	43-44	2	56
β-strand	51-54	4	57
β-strand	56	1	57
β-strand	59-61	3	58
β-strand	64	1	59
α-helix	66-71	6
α-helix	77-78	2
β-strand	84	1	60
β-strand	87-89	3	58
β-strand	95	1	59
β-strand	100-102	3	61
α-helix	105-111	7
β-strand	115	1	60
β-strand	117-122	6	61
α-helix	125A-126	3
β-strand	130-131	2	62
β-strand	136-140	5	63
β-strand	145-146	2	63
β-strand	151-153	3	61
β-strand	155-156	2	62
β-strand	157	1	64
β-strand	160	1	64
α-helix	162-163	2
β-strand	164-169	6	65
β-strand	175-184	10	61
α-helix	188-195	8
β-strand	202-205	4	65
β-strand	210-213	4	65
β-strand	223	1	66
β-strand	226	1	66
β-strand	229-237	9	61
β-strand	242-247	6	65
β-strand	251-254	4	61
β-strand	256-260A	6	61
β-strand	267-269	3	58
α-helix	272-273	2
β-strand	274-279	6	57
β-strand	281-283	3	67
β-strand	286-288	3	67
β-strand	294-295	2	56
β-strand	302-304	3	67
α-helix	306	1
β-strand	307-308	2	56
β-strand	315-317	3	55
β-strand	321	1	54

Chains H, J and N: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	14	1	52
β-strand	22-28	7	51
β-strand	31-36	6	51
α-helix	38-57	20
β-strand	63-65	3	67
α-helix	75-126	52
α-helix	127-129	3
β-strand	130-132	3	51
β-strand	137-140	4	51
α-helix	146-154	9
α-helix	159-172	14

8 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
Hemagglutinin HA1	A, C, E, G, I, K, M, O, Q	protein	325	Influenza A virus	A0A8E4ZAK5
Hemagglutinin HA2	B, D, F, H, J, L, N, P, R	protein	176	Influenza A virus	A0A8K1XY81

Sequence of entity 1 (A, C, E, G, I, K, M, O, Q), FASTA

>9DIO_1 Hemagglutinin HA1 (chains A, C, E, G, I, K, M, O, Q)
ADPGDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCS
VAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKIQI
IPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILW
GIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGLRGRMDFFWTILKPD
DAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHP
LTIGECPKYVKSNKLVLATGLRNSP

Sequence of entity 2 (B, D, F, H, J, L, N, P, R), FASTA

>9DIO_2 Hemagglutinin HA2 (chains B, D, F, H, J, L, N, P, R)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREEISSG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	16

Primary citation

A single mutation in bovine influenza H5N1 hemagglutinin switches specificity to human receptors. Lin, T.H., Zhu, X., Wang, S. et al. Science (2024) 386:1128-1134. DOI 10.1126/science.adt0180 · PubMed

Other PDB entries of the same protein (UniProt A0A8E4ZAK5), best resolution first:

8X2D 2.48 Å, Crystal structure of H5 hemagglutinin from swan-infecting H5N8 influenza virus complexed…
8X2C 2.59 Å, Crystal structure of H5 hemagglutinin from swan-infecting H5N8 influenza virus
8X29 2.61 Å, Crystal structure of H5 hemagglutinin from swan-infecting H5N8 influenza virus in…
8X2F 2.62 Å, Cryo-EM structure of H5 hemagglutinin from human-infecting H5N8 influenza virus in…
9EKF 2.68 Å, CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab 65C6 and an auto glycan…
8ZDV 2.8 Å, The cryoEM structure of H5N8 HA in an auto inhibited state
9DWE 2.8 Å, Cryo-EM structure of hemagglutinin H5 A/Texas/37/2024 in complex with LSTa and antibody…
9JN0 2.84 Å, Cryo-EM structure of a human-infecting bovine influenza H5N1 hemagglutinin complexed…
9JMZ 2.91 Å, Cryo-EM structure of a human-infecting bovine influenza H5N1 hemagglutinin complexed…
9N7T 3.01 Å, H5 hemagglutinin (A/Jiangsu/NJ210/2023) in complex with central stem-targeting Fab ST14
8X27 3.04 Å, Crystal structure of H5 hemagglutinin from human-infecting H5N8 influenza virus in…
9MQ2 3.06 Å, Cryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12G1

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