9M4P: Alpha-hemolysin

Cryo-EM structure of alpha-hemolysin heptameric pore state in the presence of RBC. Determined by electron microscopy at 3.1 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 16,415
Mol. weight: 233.03 kDa
Released: 26 Nov 2025

Explore 9M4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M4P contains 24 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: 4 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	153-158	6	11
β-strand	165-171	7	11
β-strand	174-175	2	12
α-helix	180	1
β-strand	181-182	2	12
β-strand	192	1	11
α-helix	218-221	4
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	279-285	7	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	132-151	20	6
β-strand	153-158	6	16
β-strand	165-171	7	16
β-strand	174-175	2	17
β-strand	181-182	2	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

Chains C and G: 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	109-127	19	6
β-strand	132-151	20	6
β-strand	153-158	6	21
β-strand	165-171	7	21
β-strand	174-175	2	22
β-strand	181-182	2	22
β-strand	192	1	21
α-helix	218-221	4
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	279-285	7	21
β-strand	290-292	3	21

Chain E: 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	153-158	6	31
β-strand	164-171	8	31
β-strand	174-175	2	32
β-strand	181-182	2	32
β-strand	192	1	31
α-helix	218-221	4
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	P09616 (AlphaFold model)

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

>9M4P_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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