9KRE: Alpha-hemolysin

Alpha-hemolysin heptameric POPC bound pore state derived from egg PC/Cholesterol (3:1 molar ratio) liposomes. Determined by electron microscopy at 3.0 Å resolution. Released 11 Jun 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 16,842
Mol. weight: 238.35 kDa
Ligands: POV
Released: 11 Jun 2025

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

Secondary structure: helices and β-sheets

9KRE 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, B, C, D, E, F and G: 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	75-89	15	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	164-171	8	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	265-270	6	11
β-strand	275-276	2	11
β-strand	279-285	7	11
β-strand	290-291	2	11

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

>9KRE_1 Alpha-hemolysin (chains A, B, C, D, E, F, G)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 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
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…
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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