9EKF: H5N1 A/Texas/37/2024 HA

CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab 65C6 and an auto glycan occupying the receptor-binding site. Determined by electron microscopy at 2.68 Å resolution. Released 18 Dec 2024.

Method: Electron microscopy
Resolution: 2.68 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 9
Atoms: 17,537
Mol. weight: 351.01 kDa
Ligands: NAG
Released: 18 Dec 2024

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

Secondary structure: helices and β-sheets

9EKF contains 44 α-helices and 217 β-strands across 9 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: 14 helices, 51 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	1
β-strand	12	1	2
β-strand	18-20	3	3
β-strand	28-30	3	3
β-strand	33-35	3	4
β-strand	37-38	2	5
β-strand	45-48	4	6
β-strand	51	1	6
α-helix	52-53	2
β-strand	54-55	2	7
β-strand	59	1	8
α-helix	61-66	6
α-helix	69-74	6
β-strand	83-85	3	7
β-strand	91	1	8
β-strand	97-99	3	9
α-helix	102-109	8
β-strand	112-119	8	9
α-helix	123-125	3
β-strand	130	1	10
β-strand	136-141	6	11
β-strand	144-146	3	11
β-strand	151-153	3	9
β-strand	155	1	10
α-helix	162-163	2
β-strand	164-166	3	12
β-strand	167-169	3	13
β-strand	176-184	9	9
α-helix	188-194	7
β-strand	202-205	4	12
β-strand	210-213	4	12
β-strand	223	1	14
β-strand	226	1	14
β-strand	229-237	9	9
β-strand	242	1	13
β-strand	245-247	3	12
β-strand	251-254	4	9
β-strand	256-263	8	9
β-strand	268-270	3	7
α-helix	273-274	2
β-strand	275-280	6	6
β-strand	282-284	3	15
β-strand	287-288	2	15
β-strand	295-296	2	5
β-strand	301	1	16
β-strand	303-304	2	15
α-helix	307	1
β-strand	308-309	2	5
β-strand	316-318	3	4
β-strand	322	1	3
α-helix	323-324	2
β-strand	340	1	17
β-strand	344	1	17
β-strand	348	1	2
β-strand	356-361	6	1
β-strand	362	1	18
β-strand	365	1	18
β-strand	368	1	1
α-helix	375-392	18
β-strand	399	1	16
α-helix	409-459	51
β-strand	466	1	19
β-strand	472	1	19
α-helix	480-488	9
α-helix	493-502	10

Chain B: 14 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	20
β-strand	12	1	21
β-strand	18-20	3	22
β-strand	28-30	3	22
β-strand	33-35	3	23
β-strand	37-38	2	24
β-strand	45-48	4	25
β-strand	51	1	25
α-helix	52-53	2
β-strand	54-55	2	26
β-strand	59	1	27
α-helix	61-66	6
α-helix	69-74	6
β-strand	83-85	3	26
β-strand	91	1	27
β-strand	97-99	3	28
α-helix	102-109	8
β-strand	112-119	8	28
α-helix	123-125	3
β-strand	130	1	29
β-strand	136-141	6	30
β-strand	144-146	3	30
β-strand	151-153	3	28
β-strand	155	1	29
β-strand	164-169	6	31
β-strand	176-184	9	28
α-helix	188-195	8
β-strand	202-205	4	31
β-strand	210-213	4	31
β-strand	223	1	32
β-strand	226	1	32
β-strand	229-237	9	28
β-strand	242-247	6	31
β-strand	259-262	4	28
β-strand	264-271	8	28
β-strand	276-278	3	26
α-helix	281-282	2
β-strand	283-288	6	25
β-strand	290-292	3	33
β-strand	295-296	2	33
β-strand	303-304	2	24
β-strand	309	1	34
β-strand	311-312	2	33
α-helix	315	1
β-strand	316-317	2	24
β-strand	324-326	3	23
β-strand	330	1	22
α-helix	331-332	2
β-strand	348	1	35
β-strand	352	1	35
β-strand	356	1	21
β-strand	364-370	7	20
β-strand	373-375	3	20
β-strand	378	1	20
α-helix	383-400	18
β-strand	407	1	34
α-helix	417-468	52
β-strand	474	1	36
β-strand	480	1	36
α-helix	488-496	9
α-helix	501-503	3
α-helix	507-511	5

Chain C: 13 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	37
β-strand	12	1	38
β-strand	19-20	2	39
β-strand	28-29	2	39
β-strand	30	1	40
β-strand	33-35	3	41
β-strand	37-38	2	42
β-strand	45-48	4	43
β-strand	51	1	43
α-helix	52-53	2
β-strand	54-55	2	44
β-strand	59	1	45
α-helix	61-66	6
α-helix	69-74	6
β-strand	83-85	3	44
β-strand	91	1	45
β-strand	97-99	3	46
α-helix	102-109	8
β-strand	112-119	8	46
α-helix	123-125	3
β-strand	130	1	47
β-strand	136-141	6	48
β-strand	144-146	3	48
β-strand	151-153	3	46
β-strand	155	1	47
β-strand	164-166	3	49
β-strand	167-169	3	50
β-strand	176-184	9	46
α-helix	188-194	7
β-strand	202-205	4	49
β-strand	210-213	4	49
β-strand	223	1	51
β-strand	226	1	51
β-strand	229-237	9	46
β-strand	242	1	50
β-strand	245-247	3	49
β-strand	259-262	4	46
β-strand	264-271	8	46
β-strand	276-278	3	44
α-helix	281-282	2
β-strand	283-288	6	43
β-strand	290-292	3	52
β-strand	295-296	2	52
β-strand	303-304	2	42
β-strand	309	1	53
β-strand	311-312	2	52
α-helix	315	1
β-strand	316-317	2	42
β-strand	324-326	3	41
β-strand	330	1	40
α-helix	331-332	2
β-strand	348	1	54
β-strand	352	1	54
β-strand	356	1	38
β-strand	364-369	6	37
β-strand	370	1	55
β-strand	373	1	55
β-strand	376-378	3	37
α-helix	383-400	18
β-strand	407	1	53
α-helix	417-468	52
β-strand	474	1	56
β-strand	480	1	56
α-helix	488-494	7
α-helix	501-511	11

Chains D, G and H: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	57
β-strand	18-23	6	57
β-strand	32-39	8	58
β-strand	45-52	8	58
β-strand	56-59	4	58
β-strand	67-72	6	57
β-strand	77-82	6	57
α-helix	84-86	3
β-strand	89-96	8	58
β-strand	99-100A	3	31
β-strand	100E-100F	2	31
β-strand	102-103	2	58

Chains I, K and L: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	63
β-strand	10-13	4	58
β-strand	19-24	6	63
β-strand	33-38	6	58
β-strand	45-49	5	58
β-strand	53-54	2	58
β-strand	62-67	6	63
β-strand	70-75	6	63
β-strand	85-90	6	58
β-strand	97-98	2	58
β-strand	102-106	5	58

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, B, C	protein	576	Influenza A virus	A0A8E4ZAK5
Fab 65C6 Heavy Chain	D, G, H	protein	237	Homo sapiens
Fab 65C6 Light Chain	I, K, L	protein	214	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>9EKF_1 Hemagglutinin (chains A, B, C)
MENIVLLLAIVSLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDL
NGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERANPANDLCYPGSLNDYEELKHM
LSRINHFEKIQIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISY
NNTNREDLLILWGIHHSNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGQRG
RMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGA
INSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSPLRRRRRRGLFGAIAGFIEGGWQG
MVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERR
IENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNG
CFEFYHKCDNECMESVRNGTYDYPQYSEEARLKREGSSGSSGYIPEAPRDGQAYVRKDGE
WVLLSTFLGHHHHHHHHHGGSGLNDIFEAQKIEWHE

Sequence of entity 2 (D, G, H), FASTA

>9EKF_2 Fab 65C6 Heavy Chain (chains D, G, H)
EVQLVQSGAEVKKPGESLRISCKGFAYSSTYFWISWVRQMPGKGLEWMGRIDPTDSYINY
SPSFQGHVTISVDRSISTVYLQWSSLKASDTAMYYCAYHRRGHFYGSGSAWDWFESWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVESASCDKTHTCP

Sequence of entity 3 (I, K, L), FASTA

>9EKF_3 Fab 65C6 Light Chain (chains I, K, L)
EIVLTQSPLTLSVSPGERATLSCRASQSVSSNLAWYQQMPGQAPRLLIYGASTRATGIPA
RLSGSASGTEFTLTISSLQSEDFAVYYCQQYNNWPYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Structure of a zoonotic H5N1 hemagglutinin reveals a receptor-binding site occupied by an auto-glycan. Morano, N.C., Guo, Y., Becker, J.E. et al. Structure (2025) 33:228-233.e3. DOI 10.1016/j.str.2025.01.001 · 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…
9DIO 2.7 Å, Crystal structure of H5 hemagglutinin Q226L mutant from the influenza virus…
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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