9M4A: Alpha-hemolysin

Cryo-EM structure of pre-pore state IV of heptameric alpha-hemolysin in the presence of RBC. Determined by electron microscopy at 3.46 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.46 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 15,813
Mol. weight: 233.03 kDa
Released: 26 Nov 2025

Explore 9M4A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M4A contains 28 α-helices and 217 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: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	2
α-helix	8	1
β-strand	14	1	11
β-strand	21-22	2	12
β-strand	26-29	4	13
β-strand	34-37	4	13
β-strand	40-42	3	12
β-strand	50-51	2	14
β-strand	54-56	3	12
β-strand	59-61	3	13
β-strand	66	1	15
β-strand	70	1	15
β-strand	75-76	2	15
β-strand	79-89	11	15
β-strand	97-98	2	16
β-strand	102	1	12
β-strand	111-120	10	8
β-strand	139-149	11	8
β-strand	153-158	6	15
β-strand	164-171	8	15
β-strand	174-176	3	17
β-strand	179-182	4	17
β-strand	192	1	15
β-strand	197	1	18
α-helix	206-208	3
β-strand	210	1	18
α-helix	218-222	5
β-strand	224	1	13
β-strand	229-231	3	12
β-strand	232-233	2	16
β-strand	234-235	2	14
β-strand	242-260	19	15
β-strand	265-285	21	15
β-strand	290-292	3	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alpha-hemolysin	A, B, C, D, E, F, G	protein	293	Staphylococcus aureus	P09616 (AlphaFold model)

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

>9M4A_1 Alpha-hemolysin (chains A, B, C, D, E, F, G)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Primary citation

Stepwise assembly of alpha-hemolysin from intermediates to the mature pore in native erythrocytes. Chatterjee, A., Roy, A., Das, P.P. et al. J Cell Biol (2026) 225. DOI 10.1083/jcb.202506129 · PubMed

Other PDB entries of the same protein (UniProt P09616 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AHL 1.89 Å, Alpha-hemolysin from staphylococcus aureus
3M4D 1.9 Å, Crystal structure of the M113N mutant of alpha-hemolysin
3M2L 2.1 Å, Crystal structure of the M113F mutant of alpha-hemolysin
3M3R 2.2 Å, Crystal structure of the M113F alpha-hemolysin mutant complexed with beta-cyclodextrin
8JX2 2.2 Å, alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer
8JX3 2.2 Å, alpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head 14-mer
3M4E 2.3 Å, Crystal structure of the M113N mutant of alpha-hemolysin bound to beta-cyclodextrin
6U49 2.35 Å, Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant…
9SVZ 2.4 Å, The structure of S. aureus alpha-hemolysin in complex with a bicyclic peptide inhibitor
6U4P 2.49 Å, Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant…
6U3T 2.79 Å, Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant…
4YHD 2.8 Å, Staphylococcal alpha-hemolysin H35A mutant monomer

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