9VFW: Alpha-hemolysin

Cryo-EM structure of pre-pore state II of heptameric alpha-hemolysin in the presence of RBCs. 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: 14,455
Mol. weight: 233.03 kDa
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9VFW contains 22 α-helices and 187 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 and G: 3 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	21-23	3	11
β-strand	26-29	4	12
β-strand	34-37	4	12
β-strand	40-43	4	11
β-strand	50-57	8	11
β-strand	61	1	12
β-strand	66-71	6	13
β-strand	75-89	15	13
β-strand	97-102	6	11
α-helix	105-108	4
β-strand	111	1	14
β-strand	147	1	14
β-strand	149	1	6
β-strand	153	1	15
β-strand	156-158	3	13
β-strand	165-170	6	13
β-strand	171	1	15
β-strand	174-175	2	16
β-strand	181-182	2	16
β-strand	197	1	17
β-strand	210	1	17
α-helix	211-212	2
β-strand	224	1	12
β-strand	228-235	8	11
β-strand	244-260	17	13
β-strand	265-275	11	13
β-strand	278-285	8	13
β-strand	290-292	3	13

Chain B: 3 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	21-23	3	18
β-strand	28-29	2	19
β-strand	34-35	2	19
β-strand	40-43	4	18
β-strand	50-57	8	18
β-strand	61	1	19
β-strand	66	1	20
β-strand	70	1	20
β-strand	75-86	12	20
β-strand	87-88	2	21
β-strand	89	1	20
β-strand	97-102	6	18
α-helix	106-108	3
β-strand	111	1	22
β-strand	147	1	22
β-strand	149	1	14
β-strand	153	1	23
β-strand	156-158	3	21
β-strand	165-168	4	21
β-strand	169-170	2	20
β-strand	171	1	23
β-strand	174-175	2	24
β-strand	181-182	2	24
β-strand	197	1	25
β-strand	210	1	25
α-helix	211-212	2
β-strand	224	1	19
β-strand	228-235	8	18
β-strand	244-260	17	20
β-strand	265-275	11	20
β-strand	278-285	8	20
β-strand	290-292	3	20

Chain C: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	21-23	3	26
β-strand	26-29	4	27
β-strand	34-37	4	27
β-strand	40-43	4	26
β-strand	50-56	7	26
β-strand	61	1	27
β-strand	66-70	5	28
β-strand	75-89	15	28
β-strand	97-102	6	26
α-helix	106-108	3
β-strand	111	1	29
β-strand	147	1	29
β-strand	149	1	22
β-strand	153	1	30
β-strand	156-158	3	28
β-strand	165-170	6	28
β-strand	171	1	30
β-strand	174-175	2	31
β-strand	181-182	2	31
β-strand	197	1	32
β-strand	210	1	32
α-helix	211-212	2
β-strand	224	1	27
β-strand	229-235	7	26
β-strand	244-260	17	28
β-strand	265-285	21	28
β-strand	290-292	3	28

Chain D: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	21-23	3	33
β-strand	26-29	4	34
β-strand	34-37	4	34
β-strand	40-43	4	33
β-strand	50-57	8	33
β-strand	61	1	34
β-strand	66-70	5	35
β-strand	75-89	15	35
β-strand	97-102	6	33
α-helix	105-108	4
β-strand	111	1	36
β-strand	147	1	36
β-strand	149	1	29
β-strand	153	1	37
β-strand	156-158	3	35
β-strand	165-170	6	35
β-strand	171	1	37
β-strand	174-175	2	38
β-strand	181-182	2	38
β-strand	197	1	39
β-strand	210	1	39
α-helix	211-212	2
β-strand	224	1	34
β-strand	228-235	8	33
β-strand	244-260	17	35
β-strand	265-285	21	35
β-strand	290-292	3	35

Chain E: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	21-23	3	40
β-strand	26-29	4	41
β-strand	34-37	4	41
β-strand	40-43	4	40
β-strand	50-56	7	40
β-strand	61	1	41
β-strand	66-70	5	42
β-strand	75-89	15	42
β-strand	97-100	4	40
α-helix	105-108	4
β-strand	111	1	43
β-strand	147	1	43
β-strand	149	1	36
β-strand	153	1	44
β-strand	156-158	3	42
β-strand	165-170	6	42
β-strand	171	1	44
β-strand	174-175	2	45
β-strand	181-182	2	45
β-strand	197	1	46
β-strand	210	1	46
α-helix	211-212	2
β-strand	224	1	41
β-strand	229-235	7	40
β-strand	244-260	17	42
β-strand	265-285	21	42
β-strand	290-292	3	42

Chain F: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	21-23	3	1
β-strand	26-29	4	2
β-strand	34-37	4	2
β-strand	40-43	4	1
β-strand	50-56	7	1
β-strand	61	1	2
β-strand	66-70	5	3
β-strand	75-81	7	3
β-strand	83-84	2	4
β-strand	86	1	3
β-strand	87-88	2	5
β-strand	89	1	3
β-strand	97-102	6	1
α-helix	105-108	4
β-strand	111	1	6
β-strand	147	1	6
β-strand	149	1	7
β-strand	153	1	8
β-strand	156-158	3	5
β-strand	165-168	4	5
β-strand	169-170	2	4
β-strand	171	1	8
β-strand	174-175	2	9
β-strand	181-182	2	9
β-strand	197	1	10
β-strand	210	1	10
α-helix	211-212	2
α-helix	218-222	5
β-strand	224	1	2
β-strand	229-235	7	1
β-strand	244-260	17	3
β-strand	265-285	21	3
β-strand	290-292	3	3

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

>9VFW_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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