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

Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85647. 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: 15,200
Mol. weight: 331.43 kDa
Ligands: NAG
Released: 13 Nov 2024

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

Secondary structure: helices and β-sheets

9BDG contains 41 α-helices and 175 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: 7 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	1
β-strand	34-36	3	1
β-strand	39-41	3	2
β-strand	43-44	2	3
β-strand	48	1	4
β-strand	51-52	2	5
β-strand	58-61	4	6
α-helix	66-70	5
α-helix	77-79	3
β-strand	83	1	7
β-strand	86-89	4	6
β-strand	101	1	8
α-helix	105-115	11
β-strand	117	1	7
β-strand	121-122	2	9
β-strand	131	1	10
β-strand	136-141	6	11
β-strand	144-146	3	11
β-strand	151-153	3	8
β-strand	155	1	10
β-strand	157	1	12
β-strand	160	1	12
β-strand	164-169	6	13
β-strand	176-184	9	8
α-helix	188-194	7
β-strand	202-205	4	13
β-strand	210-213	4	13
β-strand	229-237	9	8
β-strand	242-247	6	13
β-strand	251-254	4	8
β-strand	256-257	2	9
β-strand	258-259	2	8
β-strand	266-269	4	6
β-strand	274-275	2	5
β-strand	281-283	3	4
β-strand	286-288	3	4
β-strand	294-295	2	3
β-strand	302	1	4
β-strand	303-304	2	14
α-helix	306	1
β-strand	307-308	2	3
β-strand	315-317	3	2
β-strand	321	1	1
α-helix	367-384	18
β-strand	390-391	2	14
α-helix	405-442	38

Chain B: 8 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	15
β-strand	34-36	3	15
β-strand	40-41	2	16
β-strand	43-44	2	17
β-strand	51-52	2	18
β-strand	58-61	4	19
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	20
β-strand	86-89	4	19
β-strand	101	1	21
α-helix	105-115	11
β-strand	117	1	20
β-strand	121-122	2	22
β-strand	131	1	23
β-strand	136-141	6	24
β-strand	144-146	3	24
β-strand	151-153	3	21
β-strand	155	1	23
β-strand	157	1	25
β-strand	160	1	25
β-strand	166-169	4	26
β-strand	176-184	9	21
α-helix	188-194	7
β-strand	202-205	4	26
β-strand	210-213	4	26
β-strand	229-237	9	21
β-strand	242-245	4	26
β-strand	251-254	4	21
β-strand	256-257	2	22
β-strand	258-259	2	21
α-helix	260	1
β-strand	266-269	4	19
β-strand	274-275	2	18
β-strand	281-283	3	27
β-strand	286-288	3	27
β-strand	294-295	2	17
β-strand	302	1	27
β-strand	303-304	2	28
α-helix	306	1
β-strand	307-308	2	17
β-strand	315-316	2	16
α-helix	367-384	18
β-strand	390-391	2	28
α-helix	405-442	38

Chain C: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	24-26	3	29
β-strand	34-36	3	29
β-strand	39-41	3	30
β-strand	43-44	2	31
β-strand	53	1	32
β-strand	58-61	4	33
α-helix	66-71	6
α-helix	75-79	5
β-strand	86-89	4	33
β-strand	101	1	34
α-helix	105-115	11
β-strand	120-122	3	34
β-strand	131	1	35
β-strand	136-141	6	36
β-strand	144-146	3	36
β-strand	151-153	3	34
β-strand	155	1	35
β-strand	157	1	37
β-strand	160	1	37
α-helix	162-164	3
β-strand	166-169	4	38
β-strand	176-184	9	34
α-helix	188-195	8
β-strand	202-205	4	38
β-strand	210-213	4	38
β-strand	229-237	9	34
β-strand	242-245	4	38
β-strand	251-254	4	34
β-strand	256-259	4	34
β-strand	266-269	4	33
β-strand	278	1	32
β-strand	281-283	3	39
β-strand	286-288	3	39
β-strand	294-295	2	31
β-strand	302	1	39
α-helix	306	1
β-strand	307-308	2	31
β-strand	315-317	3	30
β-strand	321	1	29
α-helix	367-384	18
α-helix	405-442	38

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	40
β-strand	10-12	3	41
β-strand	18-25	8	40
α-helix	29-31	3
β-strand	34-39	6	41
β-strand	45-51	7	41
β-strand	58-60	3	41
α-helix	62-64	3
β-strand	68-73	6	40
β-strand	78-83	6	40
α-helix	88-90	3
β-strand	92-99	8	41
β-strand	112-114	3	41
β-strand	119-123	5	41

Chain E: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	42
β-strand	10-12	3	43
β-strand	18-25	8	42
α-helix	29-31	3
β-strand	34-40	7	43
β-strand	44-51	8	43
β-strand	58-60	3	43
α-helix	62-64	3
β-strand	68-73	6	42
β-strand	78-83	6	42
α-helix	88-90	3
β-strand	92-99	8	43
β-strand	112-115	4	43
α-helix	116-118	3
β-strand	119-123	5	43

Chain F: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	44
β-strand	10-12	3	45
β-strand	18-25	8	44
β-strand	34-40	7	45
β-strand	44-51	8	45
α-helix	53-55	3
β-strand	58-60	3	45
α-helix	62-64	3
β-strand	68-73	6	44
β-strand	78-83	6	44
α-helix	88-90	3
β-strand	92-99	8	45
β-strand	112-115	4	45
β-strand	119-123	5	45

Chain G: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	46
β-strand	10-13	4	47
β-strand	19-25	7	46
β-strand	33-38	6	47
β-strand	45-49	5	47
β-strand	53-54	2	47
α-helix	55	1
β-strand	62-67	6	46
β-strand	70-75	6	46
α-helix	80-82	3
β-strand	85-90	6	47
α-helix	96	1
β-strand	97	1	41
β-strand	98	1	47
α-helix	99-101	3
β-strand	102-106	5	47

Chain H: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	48
β-strand	10-13	4	49
β-strand	19-25	7	48
β-strand	33-38	6	49
β-strand	45-49	5	49
β-strand	53-54	2	49
α-helix	55	1
β-strand	62-67	6	48
β-strand	70-75	6	48
α-helix	80-82	3
β-strand	85-90	6	49
α-helix	98-101	4
β-strand	102-106	5	49

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, B, C	protein	514	Influenza A virus	A0A8F5JT24
Fab ADI-85647 Heavy chain	D, E, F	protein	239	Homo sapiens
Ig-like domain-containing protein	G, H, I	protein	214	Homo sapiens	Q7Z3Y4 (AlphaFold model)

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

>9BDG_1 Hemagglutinin (chains A, B, C)
QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICGSPHQILD
GGNCTLIDALLGDPQCDGFQNKEWDLFVERSRANSNCYPYDVPDYASLRSLVASSGTLEF
KNESFNWTGVKQNGTSSACIRGSSSSFFSRLNWLTSLNNIYPAQNVTMPNKEQFDKLYIW
GVHHPDTDKNQISLFAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPG
DILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRI
TYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRWQNSEG
RGQAADLKSTQAAIDQINGILNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDL
WSYNAELLVALINQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGS
IRNETYDHNVYRDEALNNRFQIKGAGSSLEVLFQ

Sequence of entity 2 (D, E, F), FASTA

>9BDG_2 Fab ADI-85647 Heavy chain (chains D, E, F)
EVQLVESGGGLVQPGRSLRLSCAASGFTFHNYAMHWVRQAPGKGLDWVTGITWNSVNVDY
ADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCVKGQVWSGYYLTHDAFDLWGQGTT
VTVSGASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGSSLEVLFQ

Sequence of entity 3 (G, H, I), FASTA

>9BDG_3 Ig-like domain-containing protein (chains G, H, I)
DIVMTQSPPSLSATVGDRVTITCRASQSISNYLNWYQQKPGKAPKLLISGASSLQLGVPS
RFSGSESGTDFTLTISSLQPEDCATYYCQQGYIMPGTFGQGTKVDIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

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…
9BDF 3.01 Å, Influenza A virus Hemagglutinin H3/Darwin/6/2021 in complex with Fab ADI-85666

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