9KTO: Alpha-hemolysin

Alpha-hemolysin heptameric late pre-pore state with bound lipids derived from 10:0 PC/Sphingomyelin liposomes. Determined by electron microscopy at 2.6 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 15,974
Mol. weight: 237 kDa
Ligands: P1O
Released: 11 Jun 2025

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

Secondary structure: helices and β-sheets

9KTO contains 35 α-helices and 194 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: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	2
α-helix	8	1
β-strand	14	1	9
β-strand	21-22	2	10
β-strand	26-29	4	11
β-strand	34-37	4	11
β-strand	40-43	4	10
β-strand	50-56	7	10
β-strand	59-61	3	11
β-strand	66	1	12
β-strand	70	1	12
β-strand	75-76	2	12
β-strand	79-89	11	12
β-strand	97-98	2	10
β-strand	102	1	10
β-strand	111-120	10	6
β-strand	139-149	11	6
β-strand	153-158	6	12
α-helix	159-160	2
β-strand	165-171	7	12
β-strand	174-175	2	13
β-strand	181-182	2	13
β-strand	192	1	12
β-strand	197	1	14
α-helix	206-208	3
β-strand	210	1	14
α-helix	218-221	4
β-strand	224	1	11
β-strand	229-235	7	10
β-strand	242-260	19	12
β-strand	265-285	21	12
β-strand	290-292	3	12

Chain B: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	9
α-helix	8	1
β-strand	14	1	15
β-strand	21-22	2	16
β-strand	26-29	4	17
β-strand	34-37	4	17
β-strand	40-42	3	16
β-strand	50-56	7	16
β-strand	59-61	3	17
β-strand	66	1	18
β-strand	70	1	18
β-strand	75-89	15	18
β-strand	97-98	2	16
β-strand	102	1	16
β-strand	111-120	10	6
β-strand	139-149	11	6
β-strand	153-158	6	18
α-helix	159-160	2
β-strand	164-171	8	18
β-strand	174-175	2	19
β-strand	181-182	2	19
β-strand	192	1	18
β-strand	197	1	20
α-helix	206-208	3
β-strand	210	1	20
α-helix	218-221	4
β-strand	224	1	17
β-strand	229-235	7	16
β-strand	242-260	19	18
β-strand	265-285	21	18
β-strand	290-292	3	18

Chain C: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	15
α-helix	8	1
β-strand	14	1	21
β-strand	21-22	2	22
β-strand	26-29	4	23
β-strand	34-37	4	23
β-strand	40-42	3	22
β-strand	50-56	7	22
β-strand	59-61	3	23
β-strand	66	1	24
β-strand	70	1	24
β-strand	75-89	15	24
β-strand	97-98	2	22
β-strand	102	1	22
β-strand	111-120	10	6
β-strand	139-149	11	6
β-strand	153-158	6	24
α-helix	159-160	2
β-strand	165-171	7	24
β-strand	174-175	2	25
β-strand	181-182	2	25
β-strand	192	1	24
β-strand	197	1	26
α-helix	206-208	3
β-strand	210	1	26
α-helix	218-221	4
β-strand	224	1	23
β-strand	229-235	7	22
β-strand	242-260	19	24
β-strand	265-285	21	24
β-strand	290-292	3	24

Chains D, E and F: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	21
α-helix	8	1
β-strand	14	1	27
β-strand	21-22	2	28
β-strand	26-29	4	29
β-strand	34-37	4	29
β-strand	40-42	3	28
β-strand	50-56	7	28
β-strand	59-61	3	29
β-strand	66	1	30
β-strand	70	1	30
β-strand	75-76	2	30
β-strand	79-89	11	30
β-strand	97-98	2	28
β-strand	102	1	28
β-strand	111-120	10	6
β-strand	139-149	11	6
β-strand	153-158	6	30
α-helix	159-160	2
β-strand	164-171	8	30
β-strand	174-175	2	31
β-strand	181-182	2	31
β-strand	192	1	30
β-strand	197	1	32
α-helix	206-208	3
β-strand	210	1	32
α-helix	218-221	4
β-strand	224	1	29
β-strand	229-235	7	28
β-strand	242-260	19	30
β-strand	265-285	21	30
β-strand	290-292	3	30

Chain G: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	1
α-helix	8	1
β-strand	14	1	2
β-strand	21-22	2	3
β-strand	26-29	4	4
β-strand	34-37	4	4
β-strand	40-42	3	3
β-strand	50-56	7	3
β-strand	59-61	3	4
β-strand	66	1	5
β-strand	70	1	5
β-strand	75-76	2	5
β-strand	79-89	11	5
β-strand	97-98	2	3
β-strand	102	1	3
β-strand	111-120	10	6
β-strand	139-149	11	6
β-strand	153-158	6	5
α-helix	159-160	2
β-strand	165-171	7	5
β-strand	174-175	2	7
β-strand	181-182	2	7
β-strand	192	1	5
β-strand	197	1	8
α-helix	206-208	3
β-strand	210	1	8
α-helix	218-221	4
β-strand	224	1	4
β-strand	229-235	7	3
β-strand	242-260	19	5
β-strand	265-285	21	5
β-strand	290-292	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-hemolysin	A, B, C, D, E, F, G	protein	293	Staphylococcus aureus	Q2G1X0 (AlphaFold model)

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

>9KTO_1 Alpha-hemolysin (chains A, B, C, D, E, F, G)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Ligands and cofactors

ID	Name	Formula	Copies
P1O	1,2-didecanoyl-sn-glycero-3-phosphocholine	C28 H57 N O8 P	7

Primary citation

Structural insights into pre-pore intermediates of alpha-hemolysin in the lipidic environment. Chatterjee, A., Roy, A., Satheesh, T. et al. Nat Commun (2025) 16:6348-6348. DOI 10.1038/s41467-025-61741-x · PubMed

Other PDB entries of the same protein (UniProt Q2G1X0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9SHR 2.08 Å, Alpha-Hemolysin of S.aureus (monomer) in complex with the small molecule…
4U6V 2.56 Å, Mechanisms of Neutralization of a Human Anti-Alpha Toxin Antibody
9KG0 2.6 Å, Alpha-hemolysin heptameric late pre-pore state derived from 10:0 PC/Sphingomyelin…
9KG6 2.8 Å, Alpha-hemolysin heptameric pore state derived from 10:0 PC liposomes
9KRF 2.8 Å, Alpha-hemolysin heptameric pore state bound to 10:0 PC lipid chains derived from 10:0 PC…
9KG1 2.9 Å, Alpha-hemolysin heptameric pre-pore state derived from 10:0 PC liposomes.
9KTM 2.9 Å, Alpha-hemolysin heptameric pre-pore state bound to 10:PC lipid chains derived from 10:0…
9KRE 3.0 Å, Alpha-hemolysin heptameric POPC bound pore state derived from egg PC/Cholesterol (3:1…
9KG3 3.07 Å, Alpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio)…
7O1Q 3.4 Å, Amyloid beta oligomer displayed on the alpha hemolysin scaffold

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