9DBX: AG11-2F01 Fab

Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin. Determined by electron microscopy at 2.9 Å resolution. Released 3 Sept 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 12
Atoms: 17,055
Mol. weight: 242.78 kDa
Ligands: NAG
Released: 3 Sept 2025

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

Secondary structure: helices and β-sheets

9DBX contains 45 α-helices and 216 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.

Chain A: 7 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	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	51-53	3	6
β-strand	54	1	7
β-strand	56	1	7
β-strand	59-60	2	8
β-strand	64	1	9
α-helix	66-71	6
α-helix	74-79	6
β-strand	87-89	3	8
β-strand	95	1	9
β-strand	102	1	10
α-helix	105-111	7
β-strand	115-122	8	10
α-helix	125A-126	4
β-strand	130	1	11
β-strand	136-141	6	12
β-strand	144-146	3	12
β-strand	151-153	3	10
β-strand	156	1	11
β-strand	157	1	13
β-strand	160	1	13
β-strand	164-169	6	14
β-strand	175-183	9	10
α-helix	188-195	8
β-strand	202-205	4	14
β-strand	210-213	4	14
β-strand	223	1	15
β-strand	226	1	15
β-strand	230-237	8	10
β-strand	242-247	6	14
β-strand	251-254	4	10
β-strand	256-262	7	10
β-strand	267-269	3	8
α-helix	273	1
β-strand	274-278	5	6
β-strand	281-282	2	16
β-strand	283	1	17
β-strand	286	1	17
β-strand	294-295	2	5
β-strand	302-303	2	16
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3

Chains B, D and F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	2
β-strand	22-27	6	1
β-strand	33	1	1
β-strand	36	1	1
α-helix	38-57	20
β-strand	65	1	16
α-helix	75-125	51
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-154	9
α-helix	159-172	14

Chains C and E: 7 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	18
β-strand	18	1	19
β-strand	24-26	3	20
β-strand	34-36	3	20
β-strand	39-41	3	21
β-strand	43-44	2	22
β-strand	51-53	3	23
β-strand	54	1	24
β-strand	56	1	24
α-helix	57-58	2
β-strand	59-60	2	25
β-strand	64	1	26
α-helix	66-71	6
α-helix	74-79	6
β-strand	87-89	3	25
β-strand	95	1	26
β-strand	102	1	27
α-helix	105-111	7
β-strand	115-122	8	27
β-strand	130	1	28
β-strand	136-141	6	29
β-strand	144-146	3	29
β-strand	151-153	3	27
β-strand	156	1	28
β-strand	157	1	30
β-strand	160	1	30
β-strand	164-169	6	31
β-strand	175-183	9	27
α-helix	188-195	8
β-strand	202-205	4	31
β-strand	210-213	4	31
β-strand	223	1	32
β-strand	226	1	32
β-strand	230-237	8	27
β-strand	242-247	6	31
β-strand	251-254	4	27
β-strand	256-262	7	27
β-strand	267-269	3	25
α-helix	272-273	2
β-strand	274-278	5	23
β-strand	281-282	2	33
β-strand	283	1	34
β-strand	286	1	34
β-strand	294-295	2	22
β-strand	302-303	2	33
α-helix	306	1
β-strand	307-308	2	22
β-strand	315-317	3	21
β-strand	321	1	20

Chain H: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	52
β-strand	11-12	2	53
β-strand	18-25	8	52
β-strand	34-39	7	54
β-strand	46-51	6	54
β-strand	57-59	3	54
β-strand	69-72	4	52
β-strand	77-82	6	52
α-helix	84-86	3
β-strand	88-99	12	54
β-strand	100B-103	10	54
β-strand	107-109	3	54
β-strand	110-111	2	53

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	55
β-strand	10-12	3	56
β-strand	19-25	7	55
β-strand	34-38	5	56
β-strand	45-49	5	56
β-strand	53-54	2	56
α-helix	55	1
β-strand	62-67	6	55
β-strand	70-75	6	55
α-helix	80-82	3
β-strand	85-91	7	56
β-strand	96-98	3	56
α-helix	99-100	2
β-strand	102-105	4	56

Chains W and Y: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	57
β-strand	11	1	58
β-strand	18-25	8	57
β-strand	34-39	7	59
β-strand	46-51	6	59
β-strand	57-59	3	59
β-strand	69-72	4	57
β-strand	77-82	6	57
α-helix	84-86	3
β-strand	88-99	12	59
β-strand	100B-103	10	59
β-strand	107-109	3	59
β-strand	110	1	58

Chains X and Z: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	60
β-strand	10-12	3	61
β-strand	19-25	7	60
β-strand	34-38	5	61
β-strand	45-49	5	61
β-strand	53-54	2	61
α-helix	55	1
β-strand	62-67	6	60
β-strand	70-75	6	60
α-helix	80-82	3
β-strand	85-91	7	61
β-strand	96-98	3	61
α-helix	99-101	3
β-strand	102-105	4	61

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1 chain	A, C, E	protein	321	Influenza A virus	A7Y8I1
Hemagglutinin HA2 chain	B, D, F	protein	168	Influenza A virus	B9W1X0
Heavy chain of influenza virus hemagglutinin antibody AG11-2F01	H, W, Y	protein	125	Homo sapiens
Light chain of influenza virus hemagglutinin antibody AG11-2F01	L, X, Z	protein	105	Homo sapiens

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

>9DBX_1 Hemagglutinin HA1 chain (chains A, C, E)
DTICIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDSHNGKLCRLGIAPLQLGNCSVAGWI
LGNPECELLISRESWSYIVEKPNPENGTCYPGHFADYEELREQLSSVSSFERFEIFPKES
SWPNHTTTGVSASCSHNGESSFYKNLLWLTGKNGLYPNLSKSYANNKEKEVLVLWGVHHP
PNIGDQRALYHKENAYVSVVSSHYSRKFTPEIAKRPKVRDQEGRINYYWTLLEPGDTIIF
EANGNLIAPRYAFALSRGFGSGIINSNAPMDECDAKCQTPQGAINSSLPFQNVHPVTIGE
CPKYVRSAKLRMVTGLRNIPS

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

>9DBX_2 Hemagglutinin HA2 chain (chains B, D, F)
IAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADQKSTQNAINGITNKVNSVIEKMNTQFTA
VGKEFNKLERRMENLNKKVDDGFIDIWTYNAELLVLLENERTLDFHDSNVKNLYEKVKSQ
LKNNAKEIGNGCFEFYHKCNDECMESVKNGTYDYPKYSEESKLNREKI

Sequence of entity 3 (H, W, Y), FASTA

>9DBX_3 Heavy chain of influenza virus hemagglutinin antibody AG11-2F01 (chains H, W, Y)
QVQLQESGPGLVKPSETLSLTCAVSGNSISSEYYWAWIRQPPGMPPEWVGTIYHTGNTYY
NPSLKSRTTISMDTSKNQFSLRLRSVTAADSAVYYCARAGVTIFGLTLPNYFHHWGQGTL
VTVSS

Sequence of entity 4 (L, X, Z), FASTA

>9DBX_4 Light chain of influenza virus hemagglutinin antibody AG11-2F01 (chains L, X, Z)
IQMTQSPSTLSASVGDRVTITCRASQSISNWMAWYQQKPGKAPKLLIYKASTLESGVPSR
FSGGGSGPEFTLTISSLQPDDSATYYCQQYNSYMYTFGQGTKVEI

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

High-throughput synthesis and specificity characterization of natively paired influenza hemagglutinin antibodies with oPool + display. Ouyang, W.O., Lv, H., Liu, W. et al. Sci Transl Med (2025) 17:eadt4147-eadt4147. DOI 10.1126/scitranslmed.adt4147 · PubMed

Other PDB entries of the same protein (UniProt A7Y8I1), best resolution first:

6CF7 2.72 Å, Crystal structure of the A/Solomon Islands/3/2006(H1N1) influenza virus hemagglutinin in…
6FYT 2.8 Å, Structure of H1 (A/solomon Islands/3/06) Influenza Hemagglutinin in complex with SD38
5UGY 2.8 Å, Influenza hemagglutinin in complex with a neutralizing antibody
9CU7 2.82 Å, Structure of 16.ND.92 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus…
6OC3 2.85 Å, Crystal structure of FluA-20 Fab in complex with the head domain of H1 (A/Solomon…
7UMM 3.36 Å, H1 Solomon Islands 2006 hemagglutinin in complex with Ab109
8U44 3.41 Å, CryoEM structure of A/Solomon Islands/3/2006 H1 HA in complex with 05.GC.w2.3C10-H1_SI06
7UMN 3.6 Å, H1 Solomon Islands 2006 hemagglutinin in complex with Ab36
6XSK 3.85 Å, Cryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C12 in Complex with…
6WIZ 4.2 Å, Crystal structure of Fab 54-1G05 bound to H1 influenza hemagglutinin

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