4O5I: Broadly neutralizing antibody F045-092

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/361/2011 (H3N2) influenza hemagglutinin. Determined by X-ray diffraction at 6.5 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 6.5 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 24
Atoms: 44,305
Mol. weight: 649.14 kDa
Ligands: NAG
Released: 16 Apr 2014

Explore 4O5I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O5I contains 202 α-helices and 572 β-strands across 24 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, 40 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	51-54	4	6
β-strand	58-60	3	7
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	8
β-strand	86-89	4	7
β-strand	100-101	2	9
α-helix	105-115	11
β-strand	117	1	8
β-strand	120-122	3	9
β-strand	131	1	10
β-strand	135	1	11
β-strand	136-141	6	12
β-strand	144-146	3	12
β-strand	151-153	3	9
β-strand	155	1	10
β-strand	157	1	13
β-strand	160	1	13
α-helix	162-163	2
β-strand	164-169	6	14
β-strand	176-184	9	9
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	229-237	9	9
β-strand	242-247	6	14
β-strand	251-254	4	9
β-strand	256-259	4	9
β-strand	266-269	4	7
α-helix	272-273	2
β-strand	274-278	5	6
β-strand	281-283	3	16
β-strand	286-288	3	16
β-strand	294-295	2	5
β-strand	302-305	4	16
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
α-helix	320	1
β-strand	321	1	3
α-helix	322	1

Chains B and L: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	17
β-strand	10	1	17
β-strand	14	1	2
β-strand	22-28	7	1
β-strand	31-36	6	1
α-helix	38-55	18
α-helix	59	1
β-strand	60-62	3	16
α-helix	76-126	51
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-153	8
α-helix	159-170	12

Chains C, G and K: 9 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	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	51-54	4	23
β-strand	58-60	3	24
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	25
β-strand	86-89	4	24
β-strand	100-101	2	26
α-helix	105-115	11
β-strand	117	1	25
β-strand	120-122	3	26
β-strand	131	1	27
β-strand	135	1	28
β-strand	136-141	6	29
β-strand	144-146	3	29
β-strand	151-153	3	26
β-strand	155	1	27
β-strand	157	1	30
β-strand	160	1	30
α-helix	162-163	2
β-strand	164-169	6	31
β-strand	176-184	9	26
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	229-237	9	26
β-strand	242-247	6	31
β-strand	251-254	4	26
β-strand	256-259	4	26
β-strand	266-269	4	24
α-helix	272-273	2
β-strand	274-278	5	23
β-strand	281-283	3	33
β-strand	286-288	3	33
β-strand	294-295	2	22
β-strand	302	1	33
β-strand	303-305	3	34
α-helix	306	1
β-strand	307-308	2	22
β-strand	315-317	3	21
α-helix	320	1
β-strand	321	1	20
α-helix	322	1

Chain D: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	14	1	19
β-strand	22-28	7	18
β-strand	31-36	6	18
α-helix	38-55	18
α-helix	59	1
β-strand	60-62	3	34
α-helix	76-126	51
β-strand	130-132	3	18
β-strand	137-140	4	18
α-helix	146-153	8
α-helix	159-170	12

Chain E: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	35
β-strand	18	1	36
β-strand	24-26	3	37
β-strand	34-36	3	37
β-strand	39-41	3	38
β-strand	43-44	2	39
β-strand	51-54	4	40
β-strand	58-60	3	41
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	42
β-strand	86-89	4	41
β-strand	100-101	2	43
α-helix	105-115	11
β-strand	117	1	42
β-strand	120-122	3	43
β-strand	130-131	2	44
β-strand	135	1	45
β-strand	136-141	6	46
β-strand	144-146	3	46
β-strand	151-153	3	43
β-strand	155-156	2	44
β-strand	157	1	47
β-strand	160	1	47
α-helix	162-163	2
β-strand	164-169	6	48
β-strand	176-184	9	43
α-helix	188-195	8
β-strand	202-205	4	48
β-strand	210-213	4	48
β-strand	223	1	49
β-strand	226	1	49
β-strand	229-237	9	43
β-strand	242-247	6	48
β-strand	251-254	4	43
β-strand	256-259	4	43
β-strand	266-269	4	41
α-helix	272-273	2
β-strand	274-278	5	40
β-strand	281-283	3	50
β-strand	286-288	3	50
β-strand	294-295	2	39
β-strand	302-305	4	50
α-helix	306	1
β-strand	307-308	2	39
β-strand	315-317	3	38
α-helix	320	1
β-strand	321	1	37
α-helix	322	1

Chain F: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	51
β-strand	10	1	51
β-strand	14	1	36
β-strand	22-28	7	35
β-strand	31-36	6	35
α-helix	38-55	18
α-helix	59	1
β-strand	60-62	3	50
α-helix	76-125	50
α-helix	127-129	3
β-strand	130-132	3	35
β-strand	137-140	4	35
α-helix	146-153	8
α-helix	159-170	12

Chains H and J: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	69
β-strand	10	1	69
β-strand	14	1	53
β-strand	22-28	7	52
β-strand	31-36	6	52
α-helix	38-55	18
α-helix	59	1
β-strand	60-62	3	68
α-helix	76-126	51
α-helix	127-129	3
β-strand	130-132	3	52
β-strand	137-140	4	52
α-helix	146-153	8
α-helix	159-170	12

Chain I: 9 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	11-17	7	70
β-strand	18	1	71
β-strand	24-26	3	72
β-strand	34-36	3	72
β-strand	39-41	3	73
β-strand	43-44	2	74
β-strand	51-54	4	75
β-strand	58-60	3	76
α-helix	66-71	6
α-helix	74-79	6
β-strand	83	1	77
β-strand	86-89	4	76
β-strand	100-101	2	78
α-helix	105-115	11
β-strand	117	1	77
β-strand	120-122	3	78
β-strand	131	1	79
β-strand	135	1	80
β-strand	136-141	6	81
β-strand	144-146	3	81
β-strand	151-153	3	78
β-strand	155	1	79
β-strand	157	1	82
β-strand	160	1	82
α-helix	162-163	2
β-strand	164-169	6	83
β-strand	176-184	9	78
α-helix	188-195	8
β-strand	202-205	4	83
β-strand	210-213	4	83
β-strand	223	1	84
β-strand	226	1	84
β-strand	229-237	9	78
β-strand	242-247	6	83
β-strand	251-254	4	78
β-strand	256-259	4	78
β-strand	266-269	4	76
α-helix	272-273	2
β-strand	274-278	5	75
β-strand	282-283	2	85
β-strand	286-287	2	85
β-strand	294-295	2	74
β-strand	302	1	85
β-strand	303-305	3	86
α-helix	306	1
β-strand	307-308	2	74
β-strand	315-317	3	73
α-helix	320	1
β-strand	321	1	72
α-helix	322	1

3 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 HA1 chain	A, C, E, G, I, K	protein	323	Influenza A virus	R9U684
Hemagglutinin HA2 chain	B, D, F, H, J, L	protein	176	Influenza A virus	R9U684
Fab F045-092 heavy chain	M, O, Q, S, U, W	protein	240	Homo sapiens	S6C4S0 (AlphaFold model)
Fab F045-092 light chain	N, P, R, T, V, X	protein	216	Homo sapiens	P0DOY2 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>4O5I_1 Hemagglutinin HA1 chain (chains A, C, E, G, I, K)
ADPGATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTL
IDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFN
WTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPG
TDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLIN
STGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACP
RYVKQSTLKLATGMRNVPEKQTR

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>4O5I_2 Hemagglutinin HA2 chain (chains B, D, F, H, J, L)
GIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTN
EKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFE
KTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGV

Sequence of entity 3 (M, O, Q, S, U, W), FASTA

>4O5I_3 Fab F045-092 heavy chain (chains M, O, Q, S, U, W)
EVQLVESGAEVKKPGSSVKVSCRASGTFYKYAINWVRQAPGQGLEWMGGIIPFFGTTNYA
QKFQGRLTITADGSTNTAYMQLDSLRSEDTAVYYCAGPSITESHYCLDCAAKDYYYGLDV
WGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

Sequence of entity 4 (N, P, R, T, V, X), FASTA

>4O5I_4 Fab F045-092 light chain (chains N, P, R, T, V, X)
QSVLTQPPSASGTPGQSVTISCSGSRSNIGGNTVNWYQHLPGMAPKLLIYSSNQRSSGVP
DRFSGSKSGTSASLAISGLQSEDDADYYCASWDDSLNGVVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	12

Primary citation

Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus. Lee, P.S., Ohshima, N., Stanfield, R.L. et al. Nat Commun (2014) 5:3614-3614. DOI 10.1038/ncomms4614 · PubMed

Other PDB entries of the same protein (UniProt R9U684), best resolution first:

4WE8 2.1 Å, The crystal structure of hemagglutinin of influenza virus A/Victoria/361/2011
4WE9 2.2 Å, The crystal structure of hemagglutinin from influenza virus A/Victoria/361/2011 in…
4WEA 2.2 Å, Structure and receptor binding prefereneces of recombinant human A(H3N2) virus…

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