5JZW: Aerolysin post-prepore and quasipore

Cryo-EM structures of aerolysin post-prepore and quasipore. Determined by electron microscopy at 4.46 Å resolution. Released 13 Jul 2016.

Method: Electron microscopy
Resolution: 4.46 Å
Organism: Aeromonas hydrophila
Chains: 14
Atoms: 42,910
Mol. weight: 659.86 kDa
Released: 13 Jul 2016

Explore 5JZW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5JZW contains 204 α-helices and 413 β-strands across 14 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.

Chains A, B, C, D, E, F and G: 14 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	6-8	3
β-strand	10-12	3	1
β-strand	23-25	3	1
α-helix	26-27	2
α-helix	28-33	6
α-helix	35-40	6
β-strand	48-50	3	1
β-strand	54-56	3	1
α-helix	59-61	3
β-strand	65-67	3	1
β-strand	73-77	5	1
α-helix	89-90	2
β-strand	91-93	3	2
α-helix	100-108	9
α-helix	113-123	11
β-strand	125	1	3
β-strand	129	1	4
β-strand	132	1	4
β-strand	141-144	4	5
β-strand	149-152	4	5
β-strand	169-173	5	5
β-strand	184-186	3	2
β-strand	190-191	2	2
α-helix	192-194	3
β-strand	195-196	2	2
β-strand	199-205	7	2
β-strand	215-222	8	6
β-strand	225	1	7
β-strand	271	1	8
β-strand	274-281	8	6
β-strand	290-311	22	2
β-strand	314-319	6	5
β-strand	321	1	9
β-strand	322	1	3
β-strand	338	1	9
β-strand	342-345	4	5
α-helix	351-353	3
α-helix	356-362	7
α-helix	374-380	7
α-helix	386-392	7
β-strand	396-416	21	2

Chains H, I, K, L, M and N: 15 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	45
β-strand	19	1	46
β-strand	23	1	46
β-strand	24-25	2	45
α-helix	26-27	2
α-helix	31-34	4
α-helix	37-41	5
β-strand	48-51	4	45
β-strand	54-56	3	45
α-helix	59-61	3
β-strand	65-67	3	45
β-strand	73-76	4	45
β-strand	92	1	47
α-helix	93-95	3
β-strand	96-97	2	47
α-helix	98-106	9
α-helix	109-123	15
β-strand	125	1	48
β-strand	142-145	4	47
β-strand	148-151	4	47
β-strand	170-179	10	47
β-strand	190-191	2	49
β-strand	196-206	11	49
β-strand	217-218	2	50
β-strand	219-226	8	51
β-strand	227-233	7	52
β-strand	263-269	7	52
β-strand	272-277	6	51
β-strand	280-281	2	50
α-helix	285-286	2
β-strand	290-305	16	49
β-strand	308-318	11	47
β-strand	322	1	48
β-strand	329	1	53
β-strand	341-345	5	47
α-helix	351-353	3
α-helix	355-358	4
α-helix	359-361	3
β-strand	371	1	53
α-helix	373-380	8
α-helix	382-393	12
β-strand	397-401	5	47
β-strand	403-416	14	49
α-helix	417-419	3
β-strand	420	1	49

Chain J: 16 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3
β-strand	10-12	3	60
β-strand	19	1	61
β-strand	23	1	61
β-strand	24-25	2	60
α-helix	26-27	2
α-helix	31-34	4
α-helix	37-41	5
β-strand	48-51	4	60
β-strand	54-56	3	60
α-helix	59-61	3
β-strand	65-67	3	60
β-strand	73-76	4	60
β-strand	92	1	62
α-helix	93-95	3
β-strand	96-97	2	62
α-helix	98-106	9
α-helix	109-111	3
α-helix	113-123	11
β-strand	125	1	63
β-strand	142-145	4	62
β-strand	148-151	4	62
β-strand	170-179	10	62
β-strand	190-191	2	49
β-strand	196-206	11	49
β-strand	217-218	2	64
β-strand	219-226	8	51
β-strand	227-233	7	52
β-strand	263-269	7	52
β-strand	272-277	6	51
β-strand	280-281	2	64
α-helix	285-286	2
β-strand	290-305	16	49
β-strand	308-318	11	62
β-strand	322	1	63
β-strand	329	1	65
β-strand	341-345	5	62
α-helix	351-353	3
α-helix	355-358	4
α-helix	359-361	3
β-strand	371	1	65
α-helix	373-380	8
α-helix	382-393	12
β-strand	397-401	5	62
β-strand	403-416	14	49
α-helix	417-419	3
β-strand	420	1	49

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aerolysin	A, B, C, D, E, F, G, H, I, J, K, L, M, N	protein	424	Aeromonas hydrophila	P09167 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L, M, N), FASTA

>5JZW_1 Aerolysin (chains A, B, C, D, E, F, G, H, I, J, K, L, M, N)
AEPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPG
YNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLA
HYLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLD
PDSFKHGDVTQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRYDTATNWSKTNTYGLSEKVT
TKNKFCWPLVGETELSICIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKA
DISYPYEFKADVSYDLTLSGFLRWGGNAWYTHPDNRPNWNHTFVIGPYKDKASSIRYQWD
KRYIPGEVKWWDWNWTIQQNGLSTMQNNLARVLRPVRAGITGDFSAESQFAGNIEIGAPV
PLAA

Primary citation

Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process. Iacovache, I., De Carlo, S., Cirauqui, N. et al. Nat Commun (2016) 7:12062-12062. DOI 10.1038/ncomms12062 · 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
9FML 2.2 Å, Aerolysin heptamer in membrane inserted form reconstituted in amphipoles.
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

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