4O58: Broadly neutralizing antibody F045-092

Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/3/1975 (H3N2) influenza hemagglutinin. Determined by X-ray diffraction at 2.75 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 4
Atoms: 7,390
Mol. weight: 107.89 kDa
Ligands: NAG
Released: 16 Apr 2014

Explore 4O58 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O58 contains 26 α-helices and 94 β-strands across 4 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, 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	130-131	2	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	155-156	2	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	302-304	3	16
α-helix	306	1
β-strand	307-308	2	5
β-strand	315-317	3	4
β-strand	321	1	3

Chain B: 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
β-strand	61-62	2	16
α-helix	76-126	51
α-helix	127-129	3
β-strand	130-132	3	1
β-strand	137-140	4	1
α-helix	146-154	9
α-helix	159-170	12

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	24
β-strand	10-12	3	25
β-strand	18-24	7	24
β-strand	33-39	6	25
β-strand	46-52	7	25
β-strand	56-59	4	25
α-helix	61-63	3
β-strand	67-72	6	24
β-strand	77-82	6	24
α-helix	84-86	3
β-strand	88-94	7	25
β-strand	100C	1	11
α-helix	100H-100K	4
β-strand	102-103	2	25
β-strand	107-111	5	25
α-helix	115-116	2
β-strand	117	1	26
β-strand	120-124	5	27
β-strand	136-145	10	27
β-strand	146	1	26
β-strand	151-154	4	28
β-strand	163-165	3	27
α-helix	166-167	2
β-strand	169-170	2	27
β-strand	176-184	9	27
β-strand	194-200	7	28
α-helix	201-203	3
β-strand	205-211	7	28

Chain L: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	18
β-strand	5	1	19
β-strand	9-13	4	20
β-strand	19-24	6	19
α-helix	28-30	3
β-strand	33-38	6	20
β-strand	45-49	5	20
β-strand	53-54	2	20
α-helix	55	1
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	84-92	9	20
β-strand	95B-98	4	20
β-strand	99	1	18
β-strand	102-106	5	20
α-helix	108-110	3
β-strand	111	1	21
α-helix	112-113	2
β-strand	114-118	5	22
α-helix	122-126	5
β-strand	130-139	10	22
β-strand	140	1	21
β-strand	145-150	6	23
β-strand	153-155	3	23
β-strand	159-161	3	22
α-helix	162-164	3
β-strand	165-166	2	22
β-strand	172-180	9	22
α-helix	182-185	4
β-strand	191-196	6	23
β-strand	201-206	6	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin HA1 chain	A	protein	323	Influenza A virus	P03435
Hemagglutinin HA2 chain	B	protein	176	Influenza A virus	P03435
Fab F045-092 light chain	L	protein	216	Homo sapiens	P0DOY2 (AlphaFold model)
Fab F045-092 heavy chain	H	protein	240	Homo sapiens	S6C4S0 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4O58_1 Hemagglutinin HA1 chain (chains A)
ADPGATLCLGHHAVPNGTLVKTITNDQIEVTNATELVQSSSTGKICNNPHRILDGINCTL
IDALLGDPHCDGFQNEKWDLFVERSKAFSNCYPYDVPDYASLRSLVASSGTLEFINEGFN
WTGVTQNGGSSACKRGPDSGFFSRLNWLYKSGSTYPVQNVTMPNNDNSDKLYIWGVHHPS
TDKEQTNLYVQASGKVTVSTKRSQQTIIPNVGSRPWVRGLSSRISIYWTIVKPGDILVIN
SNGNLIAPRGYFKMRTGKSSIMRSDAPIGTCSSECITPNGSIPNDKPFQNVNKITYGACP
KYVKQNTLKLATGMRNVPEKQTR

Sequence of entity 2 (B), FASTA

>4O58_2 Hemagglutinin HA2 chain (chains B)
GIFGAIAGFIENGWEGMIDGWYGFRHQNSEGTGQAADLKSTQAAIDQINGKLNRVIEKTN
EKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFE
KTRRQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGV

Sequence of entity 3 (L), FASTA

>4O58_3 Fab F045-092 light chain (chains L)
QSVLTQPPSASGTPGQSVTISCSGSRSNIGGNTVNWYQHLPGMAPKLLIYSSNQRSSGVP
DRFSGSKSGTSASLAISGLQSEDDADYYCASWDDSLNGVVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (H), FASTA

>4O58_4 Fab F045-092 heavy chain (chains H)
EVQLVESGAEVKKPGSSVKVSCRASGTFYKYAINWVRQAPGQGLEWMGGIIPFFGTTNYA
QKFQGRLTITADGSTNTAYMQLDSLRSEDTAVYYCAGPSITESHYCLDCAAKDYYYGLDV
WGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCHHHHHH

Ligands and cofactors

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

Water and common crystallization additives (PEG, SO4) are not listed.

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 P03435), best resolution first:

6R0E 1.91 Å, Structure of F11TCR in complex with DR1 MHC Class II presenting PKYVKQNTLKLAT
8IOD 2.59 Å, Cryo-EM structure of the PG-901-bound human melanocortin receptor 5 (MC5R)-Gs complex
8INR 2.73 Å, Cryo-EM structure of the alpha-MSH-bound human melanocortin receptor 5 (MC5R)-Gs complex
8IOC 2.86 Å, Cryo-EM structure of the gamma-MSH-bound human melanocortin receptor 3 (MC3R)-Gs complex
4GMS 2.95 Å, Crystal structure of heterosubtypic Fab S139/1 in complex with influenza A H3…
8JRV 3.3 Å, Cryo-EM structure of the glucagon receptor bound to glucagon and beta-arrestin 1
8JRU 3.5 Å, Cryo-EM structure of the glucagon receptor bound to beta-arrestin 1 in ligand-free state

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