5JZT: Aerolysin pore in LMNG micelle

Cryo-EM structure of aerolysin pore in LMNG micelle. Determined by electron microscopy at 7.4 Å resolution. Released 13 Jul 2016.

Method: Electron microscopy
Resolution: 7.4 Å
Organism: Aeromonas hydrophila
Chains: 7
Atoms: 23,303
Mol. weight: 330.3 kDa
Released: 13 Jul 2016

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

Secondary structure: helices and β-sheets

5JZT contains 104 α-helices and 178 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.

Chains A, D, E and F: 15 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	11-12	2
α-helix	24-26	3
α-helix	28-32	5
α-helix	35-37	3
α-helix	38-41	4
β-strand	47-50	4	1
β-strand	54-57	4	1
β-strand	66-67	2	1
α-helix	75-78	4
β-strand	91-92	2	2
β-strand	96-97	2	2
α-helix	98-107	10
α-helix	109-113	5
α-helix	114-123	10
β-strand	128	1	3
β-strand	143-144	2	4
β-strand	150-151	2	4
β-strand	159	1	3
β-strand	162	1	3
β-strand	170	1	5
α-helix	171-173	3
β-strand	176	1	6
β-strand	186	1	2
β-strand	190-205	16	2
β-strand	216	1	7
β-strand	217-218	2	8
β-strand	219-243	25	7
β-strand	255-277	23	7
β-strand	280-281	2	8
β-strand	289-312	24	2
β-strand	313	1	6
β-strand	317-318	2	5
α-helix	322-324	3
β-strand	341-342	2	5
α-helix	353-362	10
α-helix	375-379	5
α-helix	386-393	8
β-strand	396-405	10	2
β-strand	409-416	8	2
β-strand	420-421	2	2

Chain B: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	11-12	2
α-helix	24-26	3
α-helix	28-32	5
α-helix	35-37	3
α-helix	38-41	4
β-strand	47-50	4	9
β-strand	54-57	4	9
β-strand	66-67	2	9
α-helix	75-78	4
β-strand	91-92	2	2
β-strand	96-97	2	2
α-helix	98-107	10
α-helix	109-113	5
α-helix	114-123	10
β-strand	128	1	10
β-strand	143-144	2	11
β-strand	150-151	2	11
β-strand	159	1	10
β-strand	162	1	10
β-strand	170	1	12
α-helix	171-173	3
β-strand	176	1	13
β-strand	186	1	2
β-strand	190-205	16	2
β-strand	215-243	29	7
β-strand	255-277	23	7
β-strand	280-281	2	7
β-strand	289-312	24	2
β-strand	313	1	13
β-strand	317-318	2	12
α-helix	322-324	3
β-strand	341-342	2	12
α-helix	353-362	10
α-helix	375-379	5
α-helix	386-393	8
β-strand	396-405	10	2
β-strand	409-416	8	2
β-strand	420-421	2	2

Chain C: 15 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	11-12	2
α-helix	24-26	3
α-helix	28-32	5
α-helix	35-37	3
α-helix	38-41	4
β-strand	47-50	4	14
β-strand	54-57	4	14
β-strand	66-67	2	14
α-helix	75-78	4
β-strand	91-92	2	2
β-strand	96-97	2	2
α-helix	98-107	10
α-helix	109-113	5
α-helix	114-123	10
β-strand	128	1	15
β-strand	143-144	2	16
β-strand	150-151	2	16
β-strand	159	1	15
β-strand	162	1	15
β-strand	170	1	17
α-helix	171-173	3
β-strand	176	1	18
β-strand	186	1	2
β-strand	190-205	16	2
β-strand	216	1	19
β-strand	217-243	27	7
β-strand	255-281	27	7
β-strand	289-312	24	2
β-strand	313	1	18
β-strand	317-318	2	17
α-helix	322-324	3
β-strand	341-342	2	17
α-helix	353-362	10
α-helix	375-379	5
α-helix	386-393	8
β-strand	396-405	10	2
β-strand	409-416	8	2
β-strand	420-421	2	2

Chain G: 14 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	24-26	3
α-helix	28-32	5
α-helix	35-37	3
α-helix	38-41	4
β-strand	47-50	4	38
β-strand	54-57	4	38
β-strand	66-67	2	38
α-helix	75-78	4
β-strand	91-92	2	2
β-strand	96-97	2	2
α-helix	98-107	10
α-helix	109-113	5
α-helix	114-123	10
β-strand	128	1	39
β-strand	143-144	2	40
β-strand	150-151	2	40
β-strand	159	1	39
β-strand	162	1	39
β-strand	170	1	41
α-helix	171-173	3
β-strand	176	1	42
β-strand	186	1	2
β-strand	190-205	16	2
β-strand	216	1	8
β-strand	217-218	2	37
β-strand	219-243	25	7
β-strand	255-277	23	7
β-strand	280-281	2	37
β-strand	289-312	24	2
β-strand	313	1	42
β-strand	317-318	2	41
α-helix	322-324	3
β-strand	341-342	2	41
α-helix	353-362	10
α-helix	375-379	5
α-helix	386-393	8
β-strand	396-405	10	2
β-strand	409-416	8	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	424	Aeromonas hydrophila	P09167 (AlphaFold model)

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

>5JZT_1 Aerolysin (chains A, B, C, D, E, F, G)
AEPVYPDQLRLFSLGQGVCGDKYRPVNREEAQSVKSNIVGMMGQWQISGLANGWVIMGPG
YNGEIKPGTASNTWCYPTNPVTGEIPTLSALDIPDGDEVDVQWRLVHDSANFIKPTSYLA
HYLGYAWVGGNHSQYVGEDMDVTRDGDGWVIRGNNDGGCDGYRCGDKTAIKVSNFAYNLD
PDSFKHGDVTQSDRQLVKTVVGWAVNDSDTPQSGYDVTLRYDTATNWSKTNTYGLSEKVT
TKNKFKWPLVGETELSIEIAANQSWASQNGGSTTTSLSQSVRPTVPARSKIPVKIELYKA
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

Browse structure collections

About this viewer

MolViewer shows 5JZT directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.