4O5L: Broadly neutralizing antibody F045-092

Crystal structure of broadly neutralizing antibody F045-092. Determined by X-ray diffraction at 1.5 Å resolution. Released 16 Apr 2014.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,898
Mol. weight: 49.9 kDa
Ligands: PO4
Released: 16 Apr 2014

Explore 4O5L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O5L contains 22 α-helices and 46 β-strands across 2 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 H: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-24	7	7
α-helix	32	1
β-strand	33-39	6	8
β-strand	46-52	7	8
β-strand	56-59	4	8
α-helix	61-63	3
β-strand	67-72	6	7
α-helix	73-75	3
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-94	7	8
α-helix	100H-100K	4
β-strand	102-103	2	8
β-strand	107-111	5	8
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-188	3
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11
α-helix	213-215	3

Chain L: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
β-strand	5	1	2
β-strand	9-13	4	3
β-strand	19-24	6	2
α-helix	28-30	3
β-strand	34-38	5	3
β-strand	45-49	5	3
β-strand	53-54	2	3
α-helix	55	1
β-strand	62-67	6	2
β-strand	70-75	6	2
α-helix	80-82	3
β-strand	84-92	9	3
β-strand	95B-98	4	3
β-strand	99	1	1
β-strand	102-106	5	3
α-helix	108-110	3
β-strand	111	1	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-139	10	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-155	3	6
β-strand	159-161	3	5
α-helix	162-164	3
β-strand	165-166	2	5
β-strand	172-180	9	5
α-helix	182-187	6
β-strand	191-197	7	6
β-strand	200-206	7	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fab F045-092 light chain	L	protein	230	Homo sapiens	P0DOY3 (AlphaFold model)
Fab F045-092 heavy chain	H	protein	240	Homo sapiens	A8K008 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>4O5L_1 Fab F045-092 light chain (chains L)
QSVLTQPPSASGTPGQSVTISCSGSRSNIGGNTVNWYQHLPGMAPKLLIYSSNQRSSGVP
DRFSGSKSGTSASLAISGLQSEDDADYYCASWDDSLNGVVFGGGTKLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECSARLGGGDYKDDDDK

Sequence of entity 2 (H), FASTA

>4O5L_2 Fab F045-092 heavy chain (chains H)
EVQLVESGAEVKKPGSSVKVSCRASGTFYKYAINWVRQAPGQGLEWMGGIIPFFGTTNYA
QKFQGRLTITADGSTNTAYMQLDSLRSEDTAVYYCAGPSITESHYCLDCAAKDYYYGLDV
WGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1

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 P0DOY3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4R26 2.5 Å, Crystal structure of human Fab PGT124, a broadly neutralizing and potent HIV-1…
4R2G 3.28 Å, Crystal Structure of PGT124 Fab bound to HIV-1 JRCSF gp120 core and to CD4
8XLB Clamda3 domain of human immunoglobulin

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