9FML: Aerolysin

Aerolysin heptamer in membrane inserted form reconstituted in amphipoles. Determined by electron microscopy at 2.2 Å resolution. Released 12 Feb 2025.

Method: Electron microscopy
Resolution: 2.2 Å
Organism: Aeromonas hydrophila
Chains: 7
Atoms: 23,261
Mol. weight: 363.86 kDa
Released: 12 Feb 2025

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

Secondary structure: helices and β-sheets

9FML contains 112 α-helices and 168 β-strands across 7 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: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	1
β-strand	23-25	3	1
α-helix	28-33	6
α-helix	35-40	6
β-strand	47-49	3	1
β-strand	54-57	4	1
α-helix	59-61	3
β-strand	65-67	3	1
β-strand	73-77	5	1
α-helix	84-86	3
α-helix	88-90	3
β-strand	91-96	6	2
α-helix	98-106	9
α-helix	109-113	5
α-helix	114-122	9
β-strand	125	1	3
β-strand	140-145	6	2
β-strand	148-153	6	2
β-strand	169-179	11	2
α-helix	181-183	3
β-strand	185-186	2	2
β-strand	190-206	17	2
β-strand	212	1	4
β-strand	215-247	33	5
β-strand	251-281	31	5
β-strand	285	1	4
α-helix	286	1
β-strand	289-321	33	2
β-strand	322	1	3
α-helix	323	1
β-strand	329	1	6
β-strand	338-345	8	2
α-helix	355-361	7
α-helix	365-367	3
β-strand	371	1	6
α-helix	373-380	8
α-helix	382-392	11
β-strand	396-416	21	2
β-strand	420-421	2	2

Chain B: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	7
β-strand	23-25	3	7
α-helix	28-33	6
α-helix	35-40	6
β-strand	47-49	3	7
β-strand	54-57	4	7
α-helix	59-61	3
β-strand	65-67	3	7
β-strand	72-77	6	7
α-helix	84-86	3
α-helix	88-90	3
β-strand	91-96	6	2
α-helix	98-106	9
α-helix	109-113	5
α-helix	114-122	9
β-strand	125	1	8
β-strand	140-145	6	2
β-strand	148-153	6	2
β-strand	169-179	11	2
β-strand	185-186	2	2
β-strand	190-206	17	2
β-strand	212	1	9
β-strand	215-247	33	5
β-strand	251-281	31	5
β-strand	285	1	9
β-strand	289-321	33	2
β-strand	322	1	8
α-helix	323	1
β-strand	329	1	10
β-strand	338-345	8	2
α-helix	351-353	3
α-helix	355-361	7
α-helix	365-367	3
β-strand	371	1	10
α-helix	373-380	8
α-helix	382-392	11
β-strand	396-416	21	2
β-strand	420-421	2	2

Chain C: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	11
β-strand	23-25	3	11
α-helix	28-33	6
α-helix	35-39	5
β-strand	47-49	3	11
β-strand	54-57	4	11
α-helix	59-61	3
β-strand	65-67	3	11
β-strand	72-77	6	11
α-helix	84-86	3
α-helix	88-90	3
β-strand	91-96	6	2
α-helix	98-106	9
α-helix	109-113	5
α-helix	114-122	9
β-strand	125	1	12
β-strand	140-145	6	2
β-strand	148-153	6	2
β-strand	169-179	11	2
β-strand	185-186	2	2
β-strand	190-206	17	2
β-strand	212	1	13
β-strand	215-247	33	5
β-strand	251-281	31	5
β-strand	285	1	13
β-strand	289-321	33	2
β-strand	322	1	12
α-helix	323	1
β-strand	329	1	14
β-strand	338-345	8	2
α-helix	351-353	3
α-helix	355-361	7
α-helix	365-367	3
β-strand	371	1	14
α-helix	373-380	8
α-helix	382-392	11
β-strand	396-416	21	2
β-strand	420-421	2	2

Chain D: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	15
β-strand	23-25	3	15
α-helix	28-33	6
α-helix	35-40	6
β-strand	47-49	3	15
β-strand	54-57	4	15
α-helix	59-61	3
β-strand	65-67	3	15
β-strand	72-77	6	15
α-helix	84-86	3
α-helix	88-90	3
β-strand	91-96	6	2
α-helix	98-106	9
α-helix	109-113	5
α-helix	114-122	9
β-strand	125	1	16
β-strand	140-145	6	2
β-strand	148-153	6	2
β-strand	169-179	11	2
α-helix	181-183	3
β-strand	185-186	2	2
β-strand	190-206	17	2
β-strand	212	1	17
β-strand	215-247	33	5
β-strand	251-281	31	5
β-strand	285	1	17
α-helix	286	1
β-strand	289-321	33	2
β-strand	322	1	16
α-helix	323	1
β-strand	329	1	18
β-strand	338-345	8	2
α-helix	355-361	7
α-helix	365-367	3
β-strand	371	1	18
α-helix	373-380	8
α-helix	382-392	11
β-strand	396-416	21	2
β-strand	420-421	2	2

Chain E: 17 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	19
β-strand	23-25	3	19
α-helix	28-33	6
α-helix	35-40	6
β-strand	47-49	3	19
β-strand	54-57	4	19
α-helix	59-61	3
β-strand	65-67	3	19
β-strand	73-77	5	19
α-helix	84-86	3
α-helix	88-90	3
β-strand	91-96	6	2
α-helix	98-106	9
α-helix	109-113	5
α-helix	114-122	9
β-strand	125	1	20
β-strand	140-145	6	2
β-strand	148-153	6	2
α-helix	167-168	2
β-strand	169-179	11	2
α-helix	181-183	3
β-strand	185-186	2	2
β-strand	190-206	17	2
β-strand	212	1	21
β-strand	215-247	33	5
β-strand	251-281	31	5
β-strand	285	1	21
β-strand	289-321	33	2
β-strand	322	1	20
α-helix	323	1
β-strand	329	1	22
β-strand	338-345	8	2
α-helix	351-353	3
α-helix	355-361	7
α-helix	365-367	3
β-strand	371	1	22
α-helix	373-380	8
α-helix	382-392	11
β-strand	396-416	21	2
β-strand	420-421	2	2

Chain F: 17 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	23
β-strand	23-25	3	23
α-helix	28-33	6
α-helix	35-40	6
β-strand	47-49	3	23
β-strand	54-57	4	23
α-helix	59-61	3
β-strand	65-67	3	23
β-strand	73-77	5	23
α-helix	84-86	3
α-helix	88-90	3
β-strand	91-96	6	2
α-helix	98-106	9
α-helix	109-113	5
α-helix	114-122	9
β-strand	125	1	24
β-strand	140-145	6	2
β-strand	148-153	6	2
β-strand	169-179	11	2
β-strand	185-186	2	2
β-strand	190-206	17	2
β-strand	212	1	25
β-strand	215-247	33	5
β-strand	251-281	31	5
α-helix	283-284	2
β-strand	285	1	25
α-helix	286	1
β-strand	289-321	33	2
β-strand	322	1	24
α-helix	323	1
β-strand	329	1	26
β-strand	338-345	8	2
α-helix	351-353	3
α-helix	355-361	7
α-helix	365-367	3
β-strand	371	1	26
α-helix	373-380	8
α-helix	382-392	11
β-strand	396-416	21	2
β-strand	420-421	2	2

Chain G: 16 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	27
β-strand	23-25	3	27
α-helix	28-33	6
α-helix	35-40	6
β-strand	47-49	3	27
β-strand	54-57	4	27
α-helix	59-61	3
β-strand	65-67	3	27
β-strand	72-77	6	27
α-helix	84-86	3
α-helix	88-90	3
β-strand	91-96	6	2
α-helix	98-106	9
α-helix	109-113	5
α-helix	114-122	9
β-strand	125	1	28
β-strand	140-145	6	2
β-strand	148-153	6	2
β-strand	169-179	11	2
α-helix	181-183	3
β-strand	185-186	2	2
β-strand	190-206	17	2
β-strand	212	1	29
β-strand	215-247	33	5
β-strand	251-281	31	5
β-strand	285	1	29
β-strand	289-321	33	2
β-strand	322	1	28
α-helix	323	1
β-strand	329	1	30
β-strand	338-345	8	2
α-helix	351-353	3
α-helix	355-361	7
α-helix	365-367	3
β-strand	371	1	30
α-helix	373-380	8
α-helix	382-392	11
β-strand	396-416	21	2
β-strand	420-421	2	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aerolysin	A, B, C, D, E, F, G	protein	470	Aeromonas hydrophila	P09167 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G), FASTA

>9FML_1 Aerolysin (chains A, B, C, D, E, F, G)
AEPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPG
YNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLA
HYLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLD
PDSFKHGDVTQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRYDTATNWSKTNTYGLSEKVT
TKNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKA
DISYPYEFKADVSYDLTLSGFLRWGGNAWYTHPDNRPNWNHTFVIGPYKDKASSIRYQWD
KRYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPV
PLAADSKVRRARSVDGAGQGLRLEIPLDAQELSGLGFNNVSLSVTPAANQ

Primary citation

Aerolysin Nanopore Structures Revealed at High Resolution in a Lipid Environment. Anton, J.S., Iacovache, I., Bada Juarez, J.F. et al. J Am Chem Soc (2025) 147:4984-4992. DOI 10.1021/jacs.4c14288 · PubMed

Other PDB entries of the same protein (UniProt P09167 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3G4N 2.1 Å, Crystal structure of the activated aerolysin mutant H132D
9FNQ 2.1 Å, Aerolysin double mutant K238A/K244A in styrene-maleic acid lipid particles
3C0N 2.2 Å, Crystal structure of the proaerolysin mutant Y221G at 2.2 A
9FM6 2.2 Å, Aerolysin Wildtype in styrene-maleic acid lipid particles
9FMX 2.2 Å, Aerolysin Y221G - prepore
9FNP 2.2 Å, Aerolysin mutant K238A in styrene-maleic acid lipid particles
3G4O 2.3 Å, Crystal structure of the activated aerolysin mutant H132N
9GXJ 2.3 Å, Aerolysin E254A/E258A in styrene-maleic acid lipid particles
9IGN 2.3 Å, Aerolysin E254A/E258A in styrene-maleic acid lipid particles
1Z52 2.38 Å, Proaerolysin Mutant W373L
3C0O 2.5 Å, Crystal structure of the proaerolysin mutant Y221G complexed with mannose-6-phosphate
1PRE 2.8 Å, Proaerolysin

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