9BDF: Influenza A virus Hemagglutinin H3/Darwin/6/2021

Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85666. Determined by electron microscopy at 3.01 Å resolution. Released 13 Nov 2024.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 9
Atoms: 17,167
Mol. weight: 327.9 kDa
Ligands: NAG
Released: 13 Nov 2024

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

Secondary structure: helices and β-sheets

9BDF contains 34 α-helices and 191 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: 9 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	1
β-strand	18	1	2
β-strand	24-26	3	3
β-strand	34-36	3	3
β-strand	39-41	3	4
β-strand	43-44	2	5
β-strand	58-61	4	6
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	7
β-strand	86-89	4	6
β-strand	100-101	2	8
α-helix	105-115	11
β-strand	117	1	7
β-strand	120-122	3	8
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	188-195	8
β-strand	202-205	4	12
β-strand	210-213	4	12
β-strand	229-237	9	8
β-strand	242-247	6	12
β-strand	251-254	4	8
β-strand	256-259	4	8
β-strand	266-269	4	6
β-strand	281-283	3	13
β-strand	286-287	2	13
β-strand	294-295	2	5
β-strand	302-303	2	13
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3
β-strand	343	1	2
β-strand	351-357	7	1
β-strand	360-366	7	1
α-helix	367-384	18
β-strand	391	1	13
α-helix	405-454	50
β-strand	459-462	4	1
β-strand	466-469	4	1
α-helix	475-483	9
α-helix	492-499	8

Chain B: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	14
β-strand	11-12	2	15
β-strand	18-25	8	14
β-strand	34-41	8	16
β-strand	48-53	6	16
β-strand	59-61	3	16
β-strand	69-74	6	14
β-strand	79-84	6	14
α-helix	89-91	3
β-strand	93-103	11	16
β-strand	109-115	7	16
β-strand	117	1	14
β-strand	120-122	3	16
β-strand	123-124	2	15

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11	1	18
β-strand	18-25	8	17
β-strand	34-41	8	19
β-strand	48-53	6	19
β-strand	59-61	3	19
β-strand	69-74	6	17
β-strand	79-84	6	17
α-helix	89-91	3
β-strand	93-103	11	19
β-strand	109-116	8	19
β-strand	120-122	3	19
β-strand	123	1	18

Chain D: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	20
β-strand	19-25	7	20
β-strand	33-38	6	21
β-strand	45-48	4	21
β-strand	54	1	21
α-helix	55	1
β-strand	62-67	6	20
β-strand	70-75	6	20
β-strand	85-90	6	21
β-strand	98	1	21
β-strand	102-103	2	21

Chain E: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	11-12	2	23
β-strand	18-25	8	22
β-strand	34-41	8	24
β-strand	48-53	6	24
β-strand	59-61	3	24
β-strand	69-74	6	22
β-strand	79-84	6	22
α-helix	89-91	3
β-strand	93-103	11	24
β-strand	109-116	8	24
β-strand	120-122	3	24
β-strand	123-124	2	23

Chain G: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	25
β-strand	18	1	26
β-strand	24-26	3	27
β-strand	34-36	3	27
β-strand	39-41	3	28
β-strand	43-44	2	29
β-strand	51-52	2	30
β-strand	58-60	3	31
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	32
β-strand	86-89	4	31
α-helix	90	1
β-strand	101	1	33
α-helix	105-115	11
β-strand	117	1	32
β-strand	120-122	3	33
β-strand	136-141	6	34
β-strand	144-146	3	34
β-strand	151-153	3	33
β-strand	157	1	35
β-strand	160	1	35
β-strand	164-169	6	36
β-strand	176-184	9	33
α-helix	188-195	8
β-strand	202-205	4	36
β-strand	210-213	4	36
β-strand	229-237	9	33
β-strand	242-247	6	36
β-strand	251-254	4	33
β-strand	256-259	4	33
β-strand	266-269	4	31
β-strand	274-275	2	30
β-strand	281-283	3	37
β-strand	286-287	2	37
β-strand	294-295	2	29
β-strand	302-303	2	37
α-helix	305-306	2
β-strand	307-308	2	29
β-strand	315-317	3	28
β-strand	321	1	27
β-strand	343	1	26
β-strand	351-356	6	25
β-strand	361-366	6	25
α-helix	367-384	18
β-strand	391	1	37
α-helix	405-454	50
β-strand	459-462	4	25
β-strand	466-469	4	25
α-helix	475-483	9
α-helix	492-499	8

Chain H: 9 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	38
β-strand	18	1	39
β-strand	24-26	3	40
β-strand	34-36	3	40
β-strand	39-41	3	41
β-strand	43-44	2	42
β-strand	51-52	2	43
β-strand	58-61	4	44
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	45
β-strand	86-89	4	44
β-strand	100-101	2	46
α-helix	105-115	11
β-strand	117	1	45
β-strand	120-122	3	46
β-strand	131	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	157	1	49
β-strand	160	1	49
β-strand	166-169	4	50
β-strand	176-184	9	46
α-helix	188-195	8
β-strand	202-205	4	50
β-strand	210-213	4	50
β-strand	229-237	9	46
β-strand	242-247	6	50
β-strand	251-254	4	46
β-strand	256-259	4	46
β-strand	266-269	4	44
β-strand	274-275	2	43
β-strand	281-282	2	51
β-strand	294-295	2	42
β-strand	302-304	3	51
α-helix	306	1
β-strand	307-308	2	42
β-strand	315-317	3	41
β-strand	321	1	40
β-strand	343	1	39
β-strand	351-357	7	38
β-strand	360-365	6	38
α-helix	367-382	16
β-strand	390-391	2	51
α-helix	405-454	50
β-strand	459-461	3	38
β-strand	466-469	4	38
α-helix	475-483	9
α-helix	492-499	8

Chain I: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	52
β-strand	19-25	7	52
β-strand	34-38	5	53
β-strand	45-48	4	53
β-strand	54	1	53
α-helix	55	1
β-strand	62-67	6	52
β-strand	70-75	6	52
β-strand	85-89	5	53
β-strand	98	1	53
β-strand	102-103	2	53

1 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	A, G, H	protein	514	Influenza A virus	A0A8F5JT24
ADI-85666 Fab heavy chain	B, C, E	protein	240	Homo sapiens
ADI-85666 Fab light chain	D, I, J	protein	214	Homo sapiens

Sequence of entity 1 (A, G, H), FASTA

>9BDF_1 Hemagglutinin (chains A, G, H)
QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICGSPHQILD
GGNCTLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPDYASLRSLVASSGTLEF
KNESFNWTGVKQNGTSSACIRGSSSSFFSRLNWLTSLNNIYPAQNVTMPNKEQFDKLYIW
GVHHPDTDKNQISLFAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPG
DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI
TYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRWQNSEG
RGQAADLKSTQAAIDQINGILNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDL
WSYNAELLVALINQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGS
IRNETYDHNVYRDEALNNRFQIKGAGSSLEVLFQ

Sequence of entity 2 (B, C, E), FASTA

>9BDF_2 ADI-85666 Fab heavy chain (chains B, C, E)
EVQLLESGPGLVKPSETLSLTCSLSGGFVTRNSYYLSWVRQPPGKGMEWIGYVHHSGETK
YNPSLKSRVTMSMDASKNQFSLRLRSVTAADTAVYYCARDLVEGGYIPFSYGLDVWGLGT
TVTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGSSLEVLFQ

Sequence of entity 3 (D, I, J), FASTA

>9BDF_3 ADI-85666 Fab light chain (chains D, I, J)
DIQLTQSPSSLSASVGDRVTITCRASQGIRNDLGWYQQKPGKAPERLIYAASSSLPGVPS
RFRGSGSGTEFTLTISSLQPEDSATYFCLQYHNYPRTFGPGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Primary citation

Conserved sites on the influenza H1 and H3 hemagglutinin recognized by human antibodies. Maurer, D.P., Vu, M., Ferreira Ramos, A.S. et al. Sci Adv (2025) 11:eadu9140-eadu9140. DOI 10.1126/sciadv.adu9140 · PubMed

Other PDB entries of the same protein (UniProt A0A8F5JT24), best resolution first:

11MT 2.16 Å, Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry) determined using…
11MS 2.39 Å, Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C1 symmetry) determined using…
11MV 2.47 Å, Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C3 symmetry) determined using…
11MU 2.67 Å, Influenza A virus Hemagglutinin (A/Darwin/6/2021 H3N2) (C1 symmetry) determined using…
9BDG 3.01 Å, Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647

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