9KG3: Alpha-hemolysin

Alpha-hemolysin heptameric pore state derived from egg PC/Cholesterol (3:1 molar ratio) liposomes. Determined by electron microscopy at 3.07 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 3.07 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 16,424
Mol. weight: 233.03 kDa
Released: 11 Jun 2025

Explore 9KG3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KG3 contains 19 α-helices and 204 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: 3 helices, 30 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	22-29	8	3
β-strand	34-41	8	3
β-strand	51	1	4
β-strand	54-56	3	3
β-strand	59	1	3
β-strand	61-62	2	5
β-strand	66-69	4	6
β-strand	75-89	15	6
β-strand	97-101	5	3
β-strand	109-113	5	7
β-strand	116-121	6	7
β-strand	124-127	4	7
β-strand	133-149	17	7
β-strand	153-157	5	6
β-strand	161	1	6
β-strand	164-171	8	6
β-strand	174	1	8
β-strand	182	1	8
β-strand	192	1	6
α-helix	218-221	4
β-strand	223-224	2	5
β-strand	229-233	5	3
β-strand	234	1	4
β-strand	243-248	6	6
β-strand	251-260	10	6
β-strand	265-270	6	6
β-strand	275-276	2	6
β-strand	280-285	6	6
β-strand	290-292	3	6

Chain B: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	9
α-helix	8	1
β-strand	14	1	1
β-strand	21-22	2	10
β-strand	25-27	3	11
β-strand	36-38	3	11
β-strand	40-43	4	10
β-strand	51	1	12
β-strand	52-56	5	10
β-strand	61	1	13
β-strand	66-69	4	14
β-strand	75-89	15	14
β-strand	97-102	6	10
β-strand	111-113	3	7
β-strand	116-127	12	7
β-strand	133-137	5	7
β-strand	140-151	12	7
β-strand	153-157	5	14
β-strand	164-171	8	14
β-strand	173-176	4	15
β-strand	179-183	5	15
β-strand	192	1	14
α-helix	218-222	5
β-strand	224	1	13
β-strand	229-233	5	10
β-strand	234	1	12
β-strand	242-248	7	14
β-strand	250-251	2	16
β-strand	252-260	9	14
β-strand	265-270	6	14
β-strand	276-277	2	16
β-strand	280-285	6	14
β-strand	290-291	2	14

Chain C: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	17
α-helix	8	1
β-strand	14	1	9
β-strand	21-27	7	18
β-strand	36-42	7	18
β-strand	51-56	6	18
β-strand	59	1	18
β-strand	61-62	2	19
β-strand	66	1	20
β-strand	71	1	21
β-strand	75	1	21
β-strand	76	1	20
β-strand	79	1	20
β-strand	83-89	7	20
β-strand	97-98	2	18
β-strand	111-127	17	7
β-strand	133-149	17	7
β-strand	153-157	5	20
β-strand	165-171	7	20
β-strand	175	1	22
β-strand	181	1	22
β-strand	192	1	20
α-helix	218-221	4
β-strand	223-224	2	19
β-strand	229-234	6	18
β-strand	242-248	7	20
β-strand	251-260	10	20
β-strand	265-276	12	20
β-strand	279-285	7	20
β-strand	290-291	2	20

Chain D: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	23
α-helix	8	1
β-strand	14	1	17
β-strand	21-22	2	24
β-strand	25-29	5	25
β-strand	34-38	5	25
β-strand	39-43	5	24
β-strand	51-56	6	24
β-strand	61	1	25
β-strand	66	1	26
β-strand	70-71	2	26
β-strand	75-89	15	26
β-strand	97-101	5	24
β-strand	111-127	17	7
β-strand	132-149	18	7
β-strand	153-157	5	26
β-strand	164-171	8	26
β-strand	174	1	27
β-strand	182	1	27
β-strand	192	1	26
α-helix	218-222	5
β-strand	224	1	25
β-strand	229-234	6	24
β-strand	242-248	7	26
β-strand	251-260	10	26
β-strand	265-270	6	26
β-strand	275-276	2	26
β-strand	279-285	7	26
β-strand	290-291	2	26

Chain E: 3 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	28
α-helix	8	1
β-strand	14	1	23
β-strand	20-22	3	29
β-strand	25-27	3	30
β-strand	36-38	3	30
β-strand	39-43	5	29
β-strand	51	1	31
β-strand	52-56	5	29
β-strand	59	1	30
β-strand	61	1	32
β-strand	66	1	33
β-strand	70	1	34
β-strand	75-76	2	34
β-strand	79-89	11	33
β-strand	97-102	6	29
β-strand	111-113	3	7
β-strand	117-127	11	7
β-strand	132-135	4	7
β-strand	138-141	4	7
β-strand	144-149	6	7
β-strand	153-158	6	33
β-strand	164-171	8	33
β-strand	174-175	2	35
β-strand	181-182	2	35
β-strand	192	1	34
α-helix	218-221	4
β-strand	224	1	32
β-strand	229-233	5	29
β-strand	234	1	31
β-strand	242-248	7	33
β-strand	251-255	5	33
β-strand	258-260	3	34
β-strand	265-267	3	34
β-strand	270	1	33
β-strand	275-276	2	33
β-strand	280-285	6	33
β-strand	290-292	3	33

Chain F: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	36
α-helix	8	1
β-strand	14	1	28
β-strand	21-22	2	37
β-strand	26-29	4	38
β-strand	34-37	4	38
β-strand	40-43	4	37
β-strand	51-56	6	37
β-strand	59-61	3	38
β-strand	66	1	39
β-strand	70	1	39
β-strand	75-89	15	39
β-strand	97-102	6	37
β-strand	111-127	17	7
β-strand	133-149	17	7
β-strand	153-158	6	39
β-strand	164-171	8	39
β-strand	174-175	2	40
β-strand	181-182	2	40
β-strand	192	1	39
β-strand	197	1	41
α-helix	206-208	3
β-strand	210	1	41
α-helix	218-222	5
β-strand	224	1	38
β-strand	229-234	6	37
β-strand	243-260	18	39
β-strand	265-285	21	39
β-strand	290-292	3	39

Chain G: 2 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	2
α-helix	8	1
β-strand	14	1	36
β-strand	20-22	3	42
β-strand	25-27	3	43
β-strand	36-38	3	43
β-strand	39-43	5	42
β-strand	51-56	6	42
β-strand	59	1	43
β-strand	61	1	44
β-strand	66	1	45
β-strand	70-71	2	45
β-strand	75-89	15	45
β-strand	97-100	4	42
β-strand	111-127	17	7
β-strand	133-149	17	7
β-strand	153-157	5	45
β-strand	164-171	8	45
β-strand	192	1	45
α-helix	218-222	5
β-strand	224	1	44
β-strand	229-234	6	42
β-strand	242-245	4	46
β-strand	248-260	13	45
β-strand	265-271	7	45
β-strand	276-279	4	45
β-strand	282-285	4	46
β-strand	290-292	3	46

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

>9KG3_1 Alpha-hemolysin (chains A, B, C, D, E, F, G)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

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…
9KTO 2.6 Å, Alpha-hemolysin heptameric late pre-pore state with bound lipids derived from 10:0…
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…
7O1Q 3.4 Å, Amyloid beta oligomer displayed on the alpha hemolysin scaffold

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