9KRF: Alpha-hemolysin heptameric pore state

Alpha-hemolysin heptameric pore state bound to 10:0 PC lipid chains derived from 10:0 PC liposomes. Determined by electron microscopy at 2.8 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 2.8 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 16,744
Mol. weight: 237 kDa
Ligands: P1O
Released: 11 Jun 2025

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

Secondary structure: helices and β-sheets

9KRF contains 21 α-helices and 189 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 and F: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	2
α-helix	8	1
β-strand	14	1	8
β-strand	21-22	2	9
β-strand	25-29	5	10
β-strand	34-38	5	10
β-strand	39-43	5	9
β-strand	51-56	6	9
β-strand	61	1	10
β-strand	66	1	11
β-strand	70-71	2	11
β-strand	75-76	2	11
β-strand	79-89	11	11
β-strand	97-101	5	9
β-strand	109-127	19	6
β-strand	132-151	20	6
β-strand	153-157	5	11
β-strand	165-171	7	11
β-strand	174	1	12
β-strand	182	1	12
β-strand	192	1	11
α-helix	218-222	5
β-strand	224	1	10
β-strand	229-234	6	9
β-strand	242-248	7	11
β-strand	251-260	10	11
β-strand	265-276	12	11
β-strand	280-285	6	11
β-strand	290-292	3	11

Chain B: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	8
α-helix	8	1
β-strand	14	1	13
β-strand	21-22	2	14
β-strand	25-29	5	15
β-strand	34-38	5	15
β-strand	39-43	5	14
β-strand	51-56	6	14
β-strand	61	1	15
β-strand	66	1	16
β-strand	70-71	2	16
β-strand	75-76	2	16
β-strand	79-89	11	16
β-strand	97-101	5	14
β-strand	109-127	19	6
β-strand	132-149	18	6
β-strand	153-157	5	16
β-strand	165-171	7	16
β-strand	174	1	17
β-strand	182	1	17
β-strand	192	1	16
α-helix	218-222	5
β-strand	224	1	15
β-strand	229-234	6	14
β-strand	242-248	7	16
β-strand	251-260	10	16
β-strand	265-276	12	16
β-strand	279-285	7	16
β-strand	290-292	3	16

Chain C: 3 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	13
α-helix	8	1
β-strand	14	1	18
β-strand	21-22	2	19
β-strand	25-29	5	20
β-strand	34-38	5	20
β-strand	39-43	5	19
β-strand	51-56	6	19
β-strand	61	1	20
β-strand	66	1	21
β-strand	70-71	2	21
β-strand	75-76	2	21
β-strand	79-89	11	21
β-strand	97-101	5	19
β-strand	111-127	17	6
β-strand	132-151	20	6
β-strand	153-157	5	21
β-strand	165-171	7	21
β-strand	174	1	22
β-strand	182	1	22
β-strand	192	1	21
α-helix	218-222	5
β-strand	224	1	20
β-strand	229-234	6	19
β-strand	242-248	7	21
β-strand	251-260	10	21
β-strand	265-276	12	21
β-strand	280-285	6	21
β-strand	290-292	3	21

Chains E and G: 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	28
β-strand	21-22	2	29
β-strand	25-29	5	30
β-strand	34-38	5	30
β-strand	39-43	5	29
β-strand	51-56	6	29
β-strand	61	1	30
β-strand	66	1	31
β-strand	70-71	2	31
β-strand	75-76	2	31
β-strand	79-89	11	31
β-strand	97-101	5	29
β-strand	109-127	19	6
β-strand	132-151	20	6
β-strand	153-157	5	31
β-strand	165-171	7	31
β-strand	174	1	32
β-strand	182	1	32
β-strand	192	1	31
α-helix	218-222	5
β-strand	224	1	30
β-strand	229-234	6	29
β-strand	242-248	7	31
β-strand	251-260	10	31
β-strand	265-276	12	31
β-strand	279-285	7	31
β-strand	290-292	3	31

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

>9KRF_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…
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
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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