9MBX: Alpha-hemolysin

Cryo-EM structure of alpha-hemolysin heptameric pre-pore state III in the presence of RBC. Determined by electron microscopy at 3.8 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.8 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 15,981
Mol. weight: 233.03 kDa
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9MBX contains 31 α-helices and 208 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: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	11
α-helix	8	1
β-strand	14	1	1
β-strand	21-22	2	12
β-strand	26-28	3	13
β-strand	34-37	4	13
β-strand	40-43	4	12
β-strand	51-57	7	12
β-strand	58-62	5	13
β-strand	66-70	5	14
β-strand	75-79	5	14
β-strand	81	1	14
β-strand	83-88	6	15
β-strand	89	1	16
β-strand	97-102	6	12
β-strand	109	1	17
β-strand	113	1	18
α-helix	137-139	3
β-strand	145	1	18
β-strand	151	1	8
β-strand	153-158	6	15
β-strand	165-171	7	15
β-strand	173-175	3	19
β-strand	181-183	3	19
β-strand	187-188	2	14
β-strand	192-193	2	14
α-helix	218-221	4
β-strand	223-224	2	13
β-strand	228-234	7	12
β-strand	242-247	6	16
β-strand	250-260	11	14
β-strand	265-277	13	14
β-strand	280-285	6	16
β-strand	290-292	3	16

Chain B: 4 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	20
α-helix	8	1
β-strand	14	1	11
β-strand	21-22	2	21
β-strand	26-28	3	22
β-strand	34	1	23
β-strand	35-37	3	22
β-strand	40-43	4	21
β-strand	51-57	7	21
β-strand	58	1	22
β-strand	61-62	2	23
β-strand	66-70	5	24
β-strand	75-79	5	24
β-strand	81	1	24
β-strand	83-88	6	25
β-strand	89	1	26
β-strand	97-102	6	21
β-strand	109-110	2	27
α-helix	137-139	3
β-strand	151	1	17
β-strand	153-158	6	25
β-strand	165-171	7	25
β-strand	173-175	3	28
β-strand	181-183	3	28
β-strand	187-188	2	24
β-strand	192-193	2	24
α-helix	218-221	4
β-strand	223-224	2	23
β-strand	228-234	7	21
β-strand	242-247	6	26
β-strand	250-260	11	24
β-strand	265-277	13	24
β-strand	280-285	6	26
β-strand	290-292	3	26

Chains C and E: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	29
α-helix	8	1
β-strand	14	1	20
β-strand	21-22	2	30
β-strand	26-28	3	31
β-strand	34-37	4	31
β-strand	40-43	4	30
β-strand	51-57	7	30
β-strand	58-62	5	31
β-strand	66-70	5	32
β-strand	75-79	5	32
β-strand	81	1	32
β-strand	83-88	6	33
β-strand	89	1	34
β-strand	97-102	6	30
α-helix	107-108	2
β-strand	109-110	2	35
α-helix	137-139	3
β-strand	150-151	2	27
β-strand	153-158	6	33
β-strand	165-171	7	33
β-strand	173-175	3	36
β-strand	181-183	3	36
β-strand	187-188	2	32
β-strand	192-193	2	32
α-helix	218-221	4
β-strand	223-224	2	31
β-strand	228-234	7	30
β-strand	242-247	6	34
β-strand	250-260	11	32
β-strand	265-277	13	32
β-strand	280-285	6	34
β-strand	290-292	3	34

Chain D: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	37
α-helix	8	1
β-strand	14	1	29
β-strand	21-22	2	38
β-strand	26-28	3	39
β-strand	34-37	4	39
β-strand	40-43	4	38
β-strand	51-57	7	38
β-strand	58-62	5	39
β-strand	66-70	5	40
β-strand	75-79	5	40
β-strand	81	1	40
β-strand	83-88	6	41
β-strand	89	1	42
β-strand	97-102	6	38
α-helix	107-108	2
β-strand	109-110	2	43
α-helix	137-139	3
β-strand	150-151	2	35
β-strand	153-158	6	41
β-strand	165-171	7	41
β-strand	173-175	3	44
β-strand	181-183	3	44
β-strand	187-188	2	40
β-strand	192-193	2	40
α-helix	218-221	4
β-strand	223-224	2	39
β-strand	228-234	7	38
β-strand	242-247	6	42
β-strand	249	1	41
β-strand	250-260	11	40
β-strand	265-277	13	40
β-strand	280-285	6	42
β-strand	290-292	3	42

Chain F: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	1
α-helix	8	1
β-strand	14	1	2
β-strand	21-22	2	3
β-strand	26-28	3	4
β-strand	34-37	4	4
β-strand	40-43	4	3
β-strand	51-57	7	3
β-strand	58-62	5	4
β-strand	66-70	5	5
β-strand	75-79	5	5
β-strand	81	1	5
β-strand	83-88	6	6
β-strand	89	1	7
β-strand	97-102	6	3
β-strand	109	1	8
α-helix	137-139	3
β-strand	149-151	3	9
β-strand	153-158	6	6
β-strand	165-171	7	6
β-strand	173-175	3	10
β-strand	181-183	3	10
β-strand	187-188	2	5
β-strand	192-193	2	5
α-helix	218-221	4
β-strand	223-224	2	4
β-strand	228-234	7	3
β-strand	242-247	6	7
β-strand	250-260	11	5
β-strand	265-277	13	5
β-strand	280-285	6	7
β-strand	290-292	3	7

Chain G: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	2
α-helix	8	1
β-strand	14	1	45
β-strand	21-22	2	53
β-strand	26-28	3	54
β-strand	34-37	4	54
β-strand	40-43	4	53
β-strand	51-57	7	53
β-strand	58-62	5	54
β-strand	66-70	5	55
β-strand	75-79	5	55
β-strand	81	1	55
β-strand	83-88	6	55
β-strand	89	1	56
β-strand	97-102	6	53
β-strand	109-111	3	9
α-helix	137-139	3
β-strand	150-151	2	51
β-strand	153-158	6	55
β-strand	165-171	7	55
β-strand	173-175	3	57
β-strand	181-183	3	57
β-strand	187-188	2	55
β-strand	192-193	2	55
α-helix	218-221	4
β-strand	223-224	2	54
β-strand	228-234	7	53
β-strand	242-247	6	56
β-strand	250-260	11	55
β-strand	265-277	13	55
β-strand	280-285	6	56
β-strand	290-292	3	56

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

>9MBX_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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