9JN0: Hemagglutinin

Cryo-EM structure of a human-infecting bovine influenza H5N1 hemagglutinin complexed with human receptor analog LSTc. Determined by electron microscopy at 2.84 Å resolution. Released 22 Jan 2025.

Method: Electron microscopy
Resolution: 2.84 Å
Organism: Influenza A virus (A/Indonesia/5/2005(H5N1))
Chains: 3
Atoms: 12,001
Mol. weight: 177.98 kDa
Ligands: NAG
Released: 22 Jan 2025

Explore 9JN0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9JN0 contains 33 α-helices and 145 β-strands across 3 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, 48 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	8	1	2
β-strand	14-16	3	3
β-strand	24-26	3	3
β-strand	29-31	3	4
β-strand	33-34	2	5
β-strand	41-44	4	6
β-strand	47	1	6
α-helix	48-49	2
β-strand	50-51	2	7
β-strand	55	1	8
α-helix	57-62	6
β-strand	76	1	9
β-strand	79-81	3	7
β-strand	87	1	8
β-strand	93-95	3	10
α-helix	98-104	7
β-strand	108	1	9
β-strand	110-115	6	10
α-helix	119-121	3
β-strand	126	1	11
β-strand	132-137	6	12
β-strand	140-142	3	12
β-strand	147-149	3	10
β-strand	151	1	11
β-strand	153	1	13
β-strand	156	1	13
β-strand	160-165	6	14
β-strand	171-180	10	10
α-helix	184-191	8
β-strand	198-201	4	14
β-strand	206-209	4	14
β-strand	219	1	15
β-strand	222	1	15
β-strand	225-233	9	10
β-strand	238-243	6	14
β-strand	247-250	4	10
β-strand	252-257	6	10
β-strand	264-266	3	7
α-helix	269-270	2
β-strand	271-276	6	6
β-strand	278-280	3	16
β-strand	283-285	3	16
β-strand	291-292	2	5
β-strand	299-300	2	16
α-helix	303	1
β-strand	304-305	2	5
β-strand	312-314	3	4
β-strand	318	1	3
β-strand	343	1	2
β-strand	351-356	6	1
β-strand	361-365	5	1
α-helix	367-386	20
β-strand	393-394	2	16
α-helix	404-451	48
β-strand	459-461	3	1
β-strand	466-469	4	1
α-helix	475-483	9
α-helix	488-498	11

Chain B: 13 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	17
β-strand	8	1	18
β-strand	15-16	2	19
β-strand	24-25	2	19
β-strand	26	1	20
β-strand	29-31	3	21
β-strand	33-34	2	22
β-strand	41-44	4	23
β-strand	47	1	23
β-strand	50-51	2	24
β-strand	55	1	25
α-helix	57-62	6
β-strand	76	1	26
β-strand	79-81	3	24
β-strand	87	1	25
β-strand	93-95	3	27
α-helix	98-104	7
β-strand	108	1	26
β-strand	109-115	7	27
α-helix	119-121	3
β-strand	126	1	28
β-strand	132-137	6	29
β-strand	140-142	3	29
β-strand	147-149	3	27
β-strand	151	1	28
β-strand	153	1	30
β-strand	156	1	30
β-strand	160-165	6	31
β-strand	171-180	10	27
α-helix	184-190	7
β-strand	198-201	4	31
β-strand	206-209	4	31
β-strand	219	1	32
β-strand	222	1	32
β-strand	225-233	9	27
β-strand	238-243	6	31
β-strand	247-250	4	27
β-strand	252-257	6	27
β-strand	264-266	3	24
α-helix	269-270	2
β-strand	271-276	6	23
β-strand	278-280	3	33
β-strand	283-285	3	33
β-strand	291-292	2	22
β-strand	299-300	2	33
α-helix	303	1
β-strand	304-305	2	22
β-strand	312-314	3	21
α-helix	317	1
β-strand	318	1	20
α-helix	319	1
α-helix	338-340	3
β-strand	343	1	18
β-strand	351-356	6	17
β-strand	361-365	5	17
α-helix	367-386	20
β-strand	393-394	2	33
α-helix	404-455	52
β-strand	459-461	3	17
β-strand	466-469	4	17
α-helix	475-483	9
α-helix	488-498	11

Chain C: 9 helices, 48 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	34
β-strand	8	1	35
β-strand	14-16	3	36
β-strand	24-26	3	36
β-strand	29-31	3	37
β-strand	33-34	2	38
β-strand	41-44	4	39
β-strand	47	1	39
β-strand	50-51	2	40
β-strand	55	1	41
α-helix	57-62	6
β-strand	76	1	42
β-strand	79-81	3	40
β-strand	87	1	41
β-strand	93-95	3	43
α-helix	98-105	8
β-strand	108	1	42
β-strand	110-115	6	43
α-helix	119-121	3
β-strand	126	1	44
β-strand	132-137	6	45
β-strand	140-142	3	45
β-strand	147-149	3	43
β-strand	151	1	44
β-strand	153	1	46
β-strand	156	1	46
β-strand	160-165	6	47
β-strand	171-180	10	43
α-helix	184-191	8
β-strand	198-201	4	47
β-strand	206-209	4	47
β-strand	219	1	48
β-strand	222	1	48
β-strand	225-233	9	43
β-strand	238-243	6	47
β-strand	247-250	4	43
β-strand	252-257	6	43
β-strand	264-266	3	40
α-helix	269-270	2
β-strand	271-276	6	39
β-strand	278-280	3	49
β-strand	283-285	3	49
β-strand	291-292	2	38
β-strand	299-300	2	49
β-strand	304-305	2	38
β-strand	312-314	3	37
β-strand	318	1	36
β-strand	343	1	35
β-strand	351-356	6	34
β-strand	361-365	5	34
α-helix	367-386	20
β-strand	394	1	49
α-helix	404-451	48
β-strand	459-461	3	34
β-strand	466-469	4	34
α-helix	475-483	9
α-helix	492-498	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin	A, B, C	protein	506	Influenza A virus (A/Indonesia/5/2005(H5N1))	A0A8E4ZAK5

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

>9JN0_1 Hemagglutinin (chains A, B, C)
DQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDLNGVKPLILKDCSVAGW
LLGNPMCDEFIRVPEWSYIVERANPANDLCYPGSLNDYEELKHMLSRINHFEKIQIIPKS
SWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKNDAYPTIKISYNNTNREDLLILWGIHH
SNNAEEQTNLYKNPITYISVGTSTLNQRLAPKIATRSQVNGQRGRMDFFWTILKPDDAIH
FESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGAINSSMPFHNIHPLTIG
ECPKYVKSNKLVLATGLRNSPLREKRRKRGLFGAIAGFIEGGWQGMVDGWYGYHHSNEQG
SGYAADKESTQKAIDGVTNKVNSIIDKMNTQFEAVGREFNNLERRIENLNKKMEDGFLDV
WTYNAELLVLMENERTLDFHDSNVKNLYDKVRLQLRDNAKELGNGCFEFYHKCDNECMES
VRNGTYDYPQYSEEARLKREEISGVK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Primary citation

Receptor binding, structure, and tissue tropism of cattle-infecting H5N1 avian influenza virus hemagglutinin. Song, H., Hao, T., Han, P. et al. Cell (2025) 188:919. DOI 10.1016/j.cell.2025.01.019 · 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…
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…
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

Browse structure collections

About this viewer

MolViewer shows 9JN0 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.