9N38: Leukocidin-like protein 1

Cryo EM structure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15. Determined by electron microscopy at 3.9 Å resolution. Released 4 Feb 2026.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Staphylococcus aureus, Homo sapiens
Chains: 4
Atoms: 5,677
Mol. weight: 97.7 kDa
Released: 4 Feb 2026

Explore 9N38 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N38 contains 5 α-helices and 57 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: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	1
β-strand	34-37	4	1
β-strand	38-42	5	2
β-strand	53-58	6	2
β-strand	60-62	3	1
β-strand	66-67	2	3
β-strand	76-90	15	3
β-strand	101-102	2	2
β-strand	153-154	2	3
β-strand	165	1	3
β-strand	168-172	5	3
β-strand	175-176	2	4
β-strand	181-182	2	4
β-strand	195	1	5
α-helix	214-215	2
α-helix	221-224	4
β-strand	226-227	2	1
β-strand	230-235	6	2
β-strand	247-260	14	3
β-strand	273	1	5
β-strand	274-287	14	3
β-strand	301-303	3	3

Chain B: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	49-55	7	6
β-strand	60-66	7	6
β-strand	79-87	9	6
β-strand	104-116	13	7
β-strand	123-129	7	6
β-strand	176-179	4	7
β-strand	188	1	7
β-strand	191-195	5	7
β-strand	197-199	3	8
β-strand	204-206	3	8
α-helix	232-234	3
α-helix	237-240	4
β-strand	243	1	6
β-strand	246-253	8	6
β-strand	260-274	15	7
α-helix	282-284	3
β-strand	285-286	2	7
β-strand	291-301	11	7
β-strand	308-317	10	7

Chain H: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	9
β-strand	10-11	2	10
β-strand	18-24	7	9
β-strand	34-39	6	10
β-strand	45-51	7	10
β-strand	58-60	3	10
β-strand	68-69	2	9
β-strand	72	1	9
β-strand	79-83	5	9
β-strand	92-98	7	10
β-strand	111	1	10
β-strand	115-118	4	10

Chain L: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	11
β-strand	36-38	3	12
β-strand	45-46	2	12
β-strand	48	1	13
β-strand	54	1	13
β-strand	63-67	5	11
β-strand	70-74	5	11
β-strand	85-87	3	12
β-strand	102-103	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
leukocidin-like protein 1	A	protein	311	Staphylococcus aureus	Q2FFA3 (AlphaFold model)
leukocidin-like protein 2	B	protein	319	Staphylococcus aureus	Q2FFA2 (AlphaFold model)
STAU-15 Heavy Chain	H	protein	121	Homo sapiens
STAU-15 Light Chain	L	protein	107	Homo sapiens

Sequence of entity 1 (A), FASTA

>9N38_1 leukocidin-like protein 1 (chains A)
SLKINSEIKQVSEKNLDGDTKMYTRTATTSDSQKNITQSLQFNFLTEPNYDKETVFIKAK
GTIGSGLRILDPNGYWNSTLRWPGSYSVSIQNVDDNNNTNVTDFAPKNQDESREVKYTYG
YKTGGDFSINRGGLTGNITKESNYSETISYQQPSYRTLLDQSTSHKGVGWKVEAHLINNM
GHDHTRQLTNDSDNRTKSEIFSLTRNGNLWAKDNFTPKDKMPVTVSEGFNPEFLAVMSHD
KKDKGKSQFVVHYKRSMDEFKIDWNRHGFWGYWSGENHVDKKEEKLSALYEVDWKTHNVK
FVKVLNDNEKK

Sequence of entity 2 (B), FASTA

>9N38_2 leukocidin-like protein 2 (chains B)
DSQDQNKKEHVDKSQQKDKRNVTNKDKNSTAPDDIGKNGKITKRTETVYDEKTNILQNLQ
FDFIDDPTYDKNVLLVKKQGSIHSNLKFESHKEEKNSNWLKYPSEYHVDFQVKRNRKTEI
LDQLPKNKISTAKVDSTFSYSSGGKFDSTKGIGRTSSNSYSKTISYNQQNYDTIASGKNN
NWHVHWSVIANDLKYGGEVKNRNDELLFYRNTRIATVENPELSFASKYRYPALVRSGFNP
EFLTYLSNEKSNEKTQFEVTYTRNQDILKNRPGIHYAPPILEKNKDGQRLIVTYEVDWKN
KTVKVVDKYSDDNKPYKEG

Sequence of entity 3 (H), FASTA

>9N38_3 STAU-15 Heavy Chain (chains H)
QVQLVQSGGGVVQPGRSLRLSCAASGFSFSTYDMNWVRQAPGKGLEWLSIISYDETNKYY
ADSVKGRFTISRDNSKNTLFLQMNSLKPEDSAVYHCVKVGWTLVGDGVDMWGQGTLVTVS
S

Sequence of entity 4 (L), FASTA

>9N38_4 STAU-15 Light Chain (chains L)
AIRMTQSPSSLSASVGDRVTISCRASQGISHYLAWYQQQPGKVPKLLIYAASTLQSGVPS
RFSGSGSGTDFTLTISSLQPEDVATYYCQKYNGAPFTFGPGTKVDIK

Primary citation

Cryo EM structure of LukAB (LukGH) toxin from Staphylococcus aureus in complex with neutralizing Fab STAU-15. Binshtein, E., Crowe, J.E. To be published.

Other PDB entries of the same protein (UniProt Q2FFA3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4TW1 2.8 Å, Crystal structure of the octameric pore complex of the Staphylococcus aureus…
5K59 2.84 Å, Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising…

Browse structure collections

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