9KG1: Alpha-hemolysin

Alpha-hemolysin heptameric pre-pore state derived from 10:0 PC liposomes. Determined by electron microscopy at 2.9 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 13,853
Mol. weight: 233.03 kDa
Released: 11 Jun 2025

Explore 9KG1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KG1 contains 13 α-helices and 179 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: 2 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	22-23	2	1
β-strand	26-29	4	2
β-strand	34-37	4	2
β-strand	40-41	2	1
β-strand	53-54	2	3
β-strand	60-62	3	2
β-strand	66-69	4	4
β-strand	76-79	4	4
β-strand	80-89	10	5
β-strand	97-101	5	3
β-strand	153-157	5	5
β-strand	164-171	8	5
β-strand	174	1	6
β-strand	182	1	6
β-strand	188	1	7
β-strand	192	1	7
α-helix	218-221	4
β-strand	223-224	2	2
β-strand	230-233	4	3
β-strand	246-254	9	5
β-strand	257-258	2	4
β-strand	276	1	5
β-strand	280	1	5
β-strand	283-285	3	8
β-strand	290-292	3	8

Chain B: 0 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	9
β-strand	27	1	10
β-strand	34-35	2	11
β-strand	36	1	10
β-strand	39	1	9
β-strand	55-56	2	12
β-strand	60-61	2	11
β-strand	66	1	13
β-strand	79-80	2	13
β-strand	87-89	3	14
β-strand	98-102	5	12
β-strand	155-157	3	15
β-strand	164-166	3	14
β-strand	167-169	3	15
β-strand	174-175	2	16
β-strand	181-182	2	16
β-strand	188	1	17
β-strand	191	1	13
β-strand	192	1	17
β-strand	224	1	11
β-strand	229-232	4	12
β-strand	246-248	3	14
β-strand	254-258	5	13
β-strand	267-270	4	13

Chain C: 1 helix, 29 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	18
β-strand	27-28	2	19
β-strand	34	1	20
β-strand	35-36	2	19
β-strand	37	1	21
β-strand	39-41	3	18
β-strand	48	1	22
β-strand	54-57	4	23
β-strand	58	1	21
β-strand	61-62	2	20
β-strand	66-69	4	24
β-strand	77-83	7	24
β-strand	89	1	25
β-strand	97-98	2	26
β-strand	154-157	4	24
β-strand	167-170	4	24
β-strand	175	1	27
β-strand	181	1	27
α-helix	218-221	4
β-strand	223-224	2	20
β-strand	228-231	4	23
β-strand	232-233	2	26
β-strand	246	1	25
β-strand	247	1	28
β-strand	252-257	6	24
β-strand	268-270	3	24
β-strand	275	1	24
β-strand	280	1	28
β-strand	284-285	2	29
β-strand	290-291	2	29

Chain D: 1 helix, 25 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	22
β-strand	27-29	3	30
β-strand	34-36	3	30
β-strand	48	1	31
β-strand	55-57	3	32
β-strand	60-61	2	30
β-strand	81-88	8	33
β-strand	97-98	2	34
β-strand	155-158	4	33
β-strand	165-170	6	33
β-strand	175	1	35
β-strand	181	1	35
β-strand	188	1	36
β-strand	191	1	37
β-strand	192	1	36
α-helix	218-221	4
β-strand	224	1	30
β-strand	228-230	3	32
β-strand	232-233	2	34
β-strand	248	1	33
β-strand	251-253	3	33
β-strand	256-260	5	37
β-strand	265-269	5	37
β-strand	275-276	2	33
β-strand	284-285	2	38
β-strand	290-291	2	38

Chain E: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	31
β-strand	26-29	4	39
β-strand	34-37	4	39
β-strand	51	1	40
β-strand	54-56	3	41
β-strand	60-61	2	39
β-strand	66-69	4	42
β-strand	76	1	43
β-strand	77-88	12	42
β-strand	89	1	44
β-strand	97-102	6	41
α-helix	106-108	3
β-strand	153-158	6	42
β-strand	165-171	7	42
β-strand	188	1	45
β-strand	192	1	45
α-helix	218-222	5
β-strand	224	1	39
β-strand	229-233	5	41
β-strand	234	1	40
β-strand	246	1	44
β-strand	251	1	46
β-strand	252-255	4	42
β-strand	258	1	43
β-strand	276	1	46

Chain F: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	47
β-strand	34	1	48
β-strand	37	1	49
β-strand	41	1	47
β-strand	48	1	50
β-strand	57	1	51
β-strand	58	1	49
β-strand	61	1	48
β-strand	66-69	4	52
β-strand	76-79	4	52
β-strand	80-89	10	53
β-strand	97-102	6	54
α-helix	106-108	3
β-strand	153-158	6	53
β-strand	166-171	6	53
β-strand	175-176	2	55
β-strand	179-181	3	55
β-strand	188	1	56
β-strand	192	1	56
β-strand	197	1	57
α-helix	206-208	3
β-strand	210	1	57
α-helix	211-212	2
β-strand	224	1	48
β-strand	228	1	51
β-strand	229-233	5	54
β-strand	243	1	58
β-strand	246-254	9	53
β-strand	257-258	2	52
β-strand	274-278	5	53
β-strand	283-285	3	58
β-strand	290-292	3	58

Chain G: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	22	1	50
β-strand	24	1	59
β-strand	27-28	2	60
β-strand	34-36	3	60
β-strand	39	1	59
β-strand	48	1	1
β-strand	53-56	4	61
β-strand	59-61	3	60
β-strand	66-69	4	62
β-strand	77-79	3	62
β-strand	80-87	8	63
β-strand	97-100	4	61
α-helix	104	1
β-strand	155-158	4	63
β-strand	166-170	5	63
α-helix	206-208	3
α-helix	218-222	5
β-strand	224	1	60
β-strand	229-233	5	61
β-strand	248	1	64
β-strand	250-254	5	63
β-strand	256-257	2	65
β-strand	260	1	66
β-strand	265	1	66
β-strand	268-269	2	65
β-strand	279	1	64
β-strand	284-285	2	67
β-strand	290-291	2	67

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

>9KG1_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…
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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