9MQ2: Cryo-EM map of H5 HA

Cryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12G1. Determined by electron microscopy at 3.06 Å resolution. Released 5 Nov 2025.

Method: Electron microscopy
Resolution: 3.06 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 8
Atoms: 13,312
Mol. weight: 223.07 kDa
Ligands: NAG
Released: 5 Nov 2025

Explore 9MQ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MQ2 contains 39 α-helices and 148 β-strands across 8 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: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	24-27	4	1
β-strand	32-35	4	1
α-helix	38-58	21
α-helix	75-126	52
β-strand	130-132	3	46
β-strand	138-140	3	46
α-helix	146-154	9

Chain A: 9 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	1
β-strand	24-26	3	2
β-strand	34-36	3	2
β-strand	40-41	2	3
β-strand	43-44	2	4
β-strand	51-54	4	5
β-strand	56	1	5
α-helix	57-58	2
β-strand	59-60	2	6
β-strand	64	1	7
α-helix	66-71	6
α-helix	77-79	3
β-strand	87-89	3	6
β-strand	94	1	7
β-strand	100-102	3	8
α-helix	105-112	8
β-strand	115-122	8	8
α-helix	125A-126	3
β-strand	131	1	9
β-strand	136-141	6	10
β-strand	144-146	3	10
β-strand	151-153	3	8
β-strand	155	1	9
β-strand	157	1	11
β-strand	160	1	11
β-strand	164-169	6	12
β-strand	176-184	9	8
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	8
α-helix	238	1
β-strand	242-247	6	12
β-strand	251-254	4	8
β-strand	256-262A	8	8
β-strand	267-269	3	6
α-helix	272-273	2
β-strand	274-279	6	5
β-strand	281-282	2	14
β-strand	294-295	2	4
β-strand	302-303	2	14
α-helix	305-306	2
β-strand	307-308	2	4
β-strand	315-316	2	3

Chain b: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	16
β-strand	23	1	47
β-strand	24-25	2	15
β-strand	28	1	48
β-strand	31	1	48
β-strand	36	1	47
α-helix	38-58	21
α-helix	75-119	45
α-helix	121-124	4
α-helix	146-154	9

Chain B: 8 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	14-15	2	15
β-strand	18	1	16
β-strand	25-26	2	17
β-strand	34-35	2	17
β-strand	39-41	3	18
β-strand	43-44	2	19
β-strand	51-54	4	20
β-strand	56	1	20
α-helix	57-58	2
β-strand	59-61	3	21
β-strand	64	1	22
α-helix	66-71	6
α-helix	77-79	3
β-strand	87-89	3	21
β-strand	94	1	22
β-strand	100-102	3	23
α-helix	105-112	8
β-strand	117-122	6	23
α-helix	125A-126	3
β-strand	131	1	24
β-strand	136-141	6	25
β-strand	144-146	3	25
β-strand	151-153	3	23
β-strand	155	1	24
β-strand	157	1	26
β-strand	160	1	26
β-strand	164-169	6	27
β-strand	175-184	10	23
α-helix	188-194	7
β-strand	202-205	4	27
β-strand	210-213	4	27
β-strand	223	1	28
β-strand	226	1	28
β-strand	229-237	9	23
β-strand	242-247	6	27
β-strand	251-254	4	23
β-strand	256-262	7	23
β-strand	267-269	3	21
α-helix	272-273	2
β-strand	274-279	6	20
β-strand	281-282	2	29
β-strand	288	1	29
β-strand	294-295	2	19
β-strand	302-303	2	29
α-helix	306	1
β-strand	307-308	2	19
β-strand	315-317	3	18

Chain c: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	30
β-strand	26-27	2	49
β-strand	32-33	2	49
α-helix	38-58	21
α-helix	75-102	28
α-helix	105-126	22
β-strand	130-132	3	50
β-strand	138-140	3	50
α-helix	146-154	9

Chain C: 6 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	30
β-strand	25-26	2	31
β-strand	34-35	2	31
β-strand	40-41	2	32
β-strand	43	1	33
β-strand	51-54	4	34
β-strand	56	1	34
β-strand	59-61	3	35
α-helix	66-71	6
β-strand	87-89	3	35
β-strand	100-102	3	36
α-helix	105-112	8
β-strand	115-122	8	36
α-helix	125A-126	3
β-strand	131	1	37
β-strand	136-141	6	38
β-strand	144-146	3	38
β-strand	151-153	3	36
β-strand	155	1	37
β-strand	164-169	6	39
β-strand	176-184	9	36
α-helix	188-194	7
β-strand	202-206	5	39
β-strand	209-213	5	39
β-strand	223	1	40
β-strand	226	1	40
β-strand	229-237	9	36
β-strand	242-247	6	39
β-strand	251-254	4	36
β-strand	256-262A	8	36
β-strand	267	1	35
α-helix	272-273	2
β-strand	274-279	6	34
β-strand	281-282	2	41
β-strand	287-288	2	41
β-strand	294-295	2	33
β-strand	302-303	2	41
α-helix	306	1
β-strand	307-308	2	33
β-strand	315-316	2	32

Chain H: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	42
β-strand	20-25	6	42
β-strand	34-39	6	43
β-strand	46-51	6	43
β-strand	57-59	3	43
β-strand	69	1	42
β-strand	72	1	42
β-strand	77-80	4	42
β-strand	88-94	7	43
β-strand	100C-100D	2	27
β-strand	102-103	2	43
α-helix	104	1
β-strand	105	1	42
α-helix	106	1
β-strand	107-109	3	43

Chain L: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	44
β-strand	19-25	7	44
β-strand	33-38	6	45
α-helix	43	1
β-strand	44-49	6	45
β-strand	53-54	2	45
β-strand	62-67	6	44
β-strand	70-75	6	44
β-strand	85-90	6	45
β-strand	97-98	2	45
α-helix	99-101	3
β-strand	102	1	45

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1	A, B, C	protein	345	Influenza A virus	A0A8E4ZAK5
12G1 Heavy Chain Fab	H	protein	122	Homo sapiens
12G1 Light Chain Fab	L	protein	111	Homo sapiens
Hemagglutinin HA2	a, b, c	protein	220	Influenza A virus	A0AAX6NNL9

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

>9MQ2_1 Hemagglutinin HA1 (chains A, B, C)
MENIVLLLAIVNLVKSDQICIGYHANNSTEQVDTIMEKNVTVTHAQDILEKTHNGKLCDL
NGVKPLILKDCSVAGWLLGNPMCDEFIRVPEWSYIVERDNPANDLCYPGSLNDYEELKHL
LSRINHFEKILIIPKSSWPNHETSLGVSAACPYQGAPSFFRNVVWLIKKDDAYPTIKISY
NNTNREDLLILWGIHHSNNAEEQTNLYKNPTTYISVGTSTLNQRLVPKIATRSQVNGQRG
RMDFFWTILKPDDAIHFESNGNFIAPEYAYKIVKKGDSTIMKSGVEYGHCNTKCQTPVGA
INSSMPFHNIHPLTIGECPKYVKSNKLVLATGLRNSPPREKRRKR

Sequence of entity 2 (H), FASTA

>9MQ2_2 12G1 Heavy Chain Fab (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGDSISSYYWSWIRQPPGKGLEWIGYVHYSGNTNYN
PSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARTTMSRGPSLYYYYGLDVWGQGTT
VT

Sequence of entity 3 (L), FASTA

>9MQ2_3 12G1 Light Chain Fab (chains L)
DIVMTQSPLSLPVTPGEPASISCRSSQSLLHSYGYIYLDWYLQKPGQSPQLLIYLGSDRA
SGIPDRFSGSGAGTDFTLKISRVEAEDVGVYYCMQALQTPITFGQGTRLEI

Sequence of entity 4 (a, b, c), FASTA

>9MQ2_4 Hemagglutinin HA2 (chains a, b, c)
GLFGAIAGFIEGGWQGMVDGWYGYHHSNEQGSGYAADKESTQKAIDGVTNKVNSIIDKMN
TQFEAVGREFNNLERRIENLNKKMEDGFLDVWTYNAELLVLMENERTLDFHDSNVKNLYD
KVRLQLRDNAKELGNGCFEFYHKCDNECMESVRNGTYYYPQYSEEARLKREEISGVGYIP
EAPRDGQAYVRKDGEWVLLSTFLGSENLYFQGGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

Primary citation

Human monoclonal antibodies that target clade 2.3.4.4b H5N1 hemagglutinin. Alzua, G.P., Leon, A.N., Yellin, T. et al. Nat Commun (2025) 17:135-135. DOI 10.1038/s41467-025-66829-y · 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…
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…

Browse structure collections

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