9N7T: H5 hemagglutinin

H5 hemagglutinin (A/Jiangsu/NJ210/2023) in complex with central stem-targeting Fab ST14. Determined by electron microscopy at 3.01 Å resolution. Released 18 Feb 2026.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 12
Atoms: 17,262
Mol. weight: 273.44 kDa
Ligands: NAG
Released: 18 Feb 2026

Explore 9N7T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N7T contains 51 α-helices and 197 β-strands across 12 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.

Chains a, I and J: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	20
β-strand	10	1	20
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-57	20
α-helix	75-126	52
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-154	9
α-helix	159-169	11

Chains A and B: 7 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	12-14	3	1
β-strand	16-17	2	1
β-strand	18	1	2
β-strand	25-26	2	3
β-strand	34-35	2	3
β-strand	39-41	3	4
β-strand	43-44	2	5
β-strand	51-54	4	6
β-strand	56	1	6
β-strand	59-60	2	7
β-strand	64	1	8
α-helix	66-71	6
α-helix	74-79	6
β-strand	87-89	3	7
β-strand	94	1	8
β-strand	100-102	3	9
α-helix	105-112	8
β-strand	117-122	6	9
α-helix	125A-126	3
β-strand	130-131	2	10
β-strand	136-141	6	11
β-strand	144-146	3	11
β-strand	151-153	3	9
β-strand	155-156	2	10
β-strand	164-169	6	12
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	13
β-strand	226	1	13
β-strand	229-237	9	9
α-helix	238	1
β-strand	242-247	6	12
β-strand	251-254	4	9
β-strand	256-262	7	9
β-strand	267-269	3	7
α-helix	272-273	2
β-strand	274-279	6	6
β-strand	281-282	2	14
β-strand	287-288	2	14
β-strand	294-295	2	5
β-strand	302-303	2	14
β-strand	307-308	2	5
β-strand	315-317	3	4

Chain C: 7 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	41
β-strand	18	1	42
β-strand	25-26	2	43
β-strand	34-35	2	43
β-strand	39-41	3	44
β-strand	43-44	2	45
β-strand	51-54	4	46
β-strand	56	1	46
β-strand	59-60	2	47
β-strand	64	1	48
α-helix	66-71	6
α-helix	74-79	6
β-strand	87-89	3	47
β-strand	94	1	48
β-strand	100-102	3	49
α-helix	105-112	8
β-strand	117-122	6	49
α-helix	125A-126	3
β-strand	130-131	2	50
β-strand	136-141	6	51
β-strand	144-146	3	51
β-strand	151-153	3	49
β-strand	155-156	2	50
β-strand	164-169	6	52
β-strand	176-184	9	49
α-helix	188-194	7
β-strand	202-205	4	52
β-strand	210-213	4	52
β-strand	223	1	53
β-strand	226	1	53
β-strand	229-237	9	49
α-helix	238	1
β-strand	242-247	6	52
β-strand	251-254	4	49
β-strand	256-262	7	49
β-strand	267-269	3	47
α-helix	272-273	2
β-strand	274-279	6	46
β-strand	281-282	2	54
β-strand	287-288	2	54
β-strand	294-295	2	45
β-strand	302-303	2	54
β-strand	307-308	2	45
β-strand	315-317	3	44

Chains D, E and H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	37
β-strand	11-12	2	38
β-strand	18-25	8	37
α-helix	29-31	3
β-strand	34-39	6	39
β-strand	45-51	7	39
β-strand	57-59	3	39
β-strand	67-72	6	37
β-strand	77-82	6	37
α-helix	84-86	3
β-strand	88-98	11	39
β-strand	100A-103	10	39
α-helix	104-106	3
β-strand	107-109	3	39
β-strand	110-111	2	38

Chains F, G and L: 3 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	35
α-helix	13-14	2
β-strand	19-24	6	35
α-helix	27-28	5
β-strand	34-38	5	36
β-strand	45-48	4	36
β-strand	62-67	6	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	85-92	8	36
β-strand	95B-98	4	36
β-strand	103	1	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H5 HA1	A, B, C	protein	345	Influenza A virus	A0A8E4ZAK5
ST14 Light Chain Fab	F, G, L	protein	110	Homo sapiens	P01704 (AlphaFold model)
ST14 Heavy Chain Fab	D, E, H	protein	124	Homo sapiens
H5 HA2	I, J, a	protein	220	Influenza A virus	A0AAX6NNL9

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

>9N7T_1 H5 HA1 (chains A, B, C)
MENIVLLLAIVNLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDL
NGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERDNPANDLCYPGSLNDYEELKHL
LSRINHFEKILIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKDDAYPTIKISY
NNTNREDLLILWGIHHSNNAEEQTNLYKNPTTYISVGTSTLNQRLVPKIATRSQVNGQRG
RMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGA
INSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSPPREKRRKR

Sequence of entity 2 (F, G, L), FASTA

>9N7T_2 ST14 Light Chain Fab (chains F, G, L)
SALTQPASVSGSPGQSITISCTGTSSDVGGYNYVSWYQQYPGKAPKVMIYEVTNRPSGVS
NRFSGSKSGNTASLTISGLQTEDEADYYCSSYTGTITHYVFGTGTKVTVL

Sequence of entity 3 (D, E, H), FASTA

>9N7T_3 ST14 Heavy Chain Fab (chains D, E, H)
QVQVVESGGGLVKPGGSLRLSCAASGFIFSDYYMSWIRQAPGKGLDWVSSITSTGSVIYY
GDSVRGRFTISRDNAKNSLYLQMNTLRAEDTAVYYCARGNTIFGIVRGWYFDLWGRGTLV
TVSS

Sequence of entity 4 (I, J, a), FASTA

>9N7T_4 H5 HA2 (chains I, J, a)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYYYPQYSEEARLKREEISGVGYIP
EAPRDGQAYVRKDGEWVLLSTFLGSENLYFQGGSHHHHHH

Ligands and cofactors

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

Primary citation

Individualized IG genotyping coupled with high throughput isolation of influenza HA-specific monoclonal antibodies. Fisher, A., Corcoran, M., Chernyshev, M. et al. To be published.

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…
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…
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

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