3M4E: M113N mutant of alpha-hemolysin

Crystal structure of the M113N mutant of alpha-hemolysin bound to beta-cyclodextrin. Determined by X-ray diffraction at 2.3 Å resolution. Released 5 May 2010.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Staphylococcus aureus
Chains: 7
Atoms: 16,774
Mol. weight: 234.06 kDa
Released: 5 May 2010

Explore 3M4E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3M4E contains 38 α-helices and 177 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: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	1
β-strand	14	1	2
β-strand	21-29	9	3
β-strand	34-43	10	3
β-strand	48	1	4
β-strand	51-61	11	3
β-strand	66-69	4	5
β-strand	75-89	15	5
β-strand	97-102	6	3
β-strand	109-121	13	6
β-strand	123-127	5	6
β-strand	134-136	3	7
β-strand	137-151	15	6
β-strand	153-157	5	5
α-helix	158-160	3
β-strand	164-171	8	5
β-strand	174-176	3	8
β-strand	179-182	4	8
β-strand	188	1	5
β-strand	192	1	5
β-strand	197	1	9
α-helix	206-208	3
β-strand	210	1	9
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	3
β-strand	228-234	7	3
β-strand	242-260	19	5
β-strand	265-285	21	5
β-strand	290-292	3	5

Chain B: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	10
β-strand	14	1	1
β-strand	21-29	9	4
β-strand	34-43	10	4
β-strand	48	1	11
β-strand	51-61	11	4
β-strand	66-69	4	12
β-strand	75-89	15	12
β-strand	97-102	6	4
α-helix	105-108	4
β-strand	109-127	19	6
β-strand	133-151	19	6
β-strand	153-158	6	12
β-strand	164-171	8	12
β-strand	174-176	3	13
β-strand	179-182	4	13
β-strand	188	1	12
β-strand	192	1	12
β-strand	197	1	14
α-helix	206-208	3
β-strand	210	1	14
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	4
β-strand	228-234	7	4
β-strand	242-260	19	12
β-strand	265-285	21	12
β-strand	290-292	3	12

Chain C: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	15
β-strand	14	1	10
α-helix	19-20	2
β-strand	21-29	9	11
β-strand	34-43	10	11
β-strand	48	1	16
β-strand	51-61	11	11
β-strand	66-69	4	17
β-strand	75-89	15	17
β-strand	97-102	6	11
β-strand	109-124	16	6
β-strand	127	1	6
β-strand	133-151	19	6
β-strand	153-157	5	17
β-strand	164-171	8	17
β-strand	174-176	3	18
β-strand	179-182	4	18
β-strand	188	1	17
β-strand	192	1	17
β-strand	197	1	19
α-helix	206-208	3
β-strand	210	1	19
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	11
β-strand	228-234	7	11
β-strand	242-260	19	17
β-strand	265-285	21	17
β-strand	290-292	3	17

Chain D: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	20
β-strand	14	1	15
β-strand	21-29	9	16
β-strand	34-43	10	16
β-strand	48	1	21
β-strand	51-61	11	16
β-strand	66-69	4	22
β-strand	75-89	15	22
β-strand	97-102	6	16
α-helix	105-108	4
β-strand	109-126	18	6
β-strand	132-133	2	6
β-strand	136-151	16	6
β-strand	153-158	6	22
β-strand	164-171	8	22
β-strand	174-176	3	23
β-strand	179-182	4	23
β-strand	188	1	22
β-strand	192	1	22
β-strand	197	1	24
α-helix	206-208	3
β-strand	210	1	24
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	16
β-strand	228-234	7	16
β-strand	242-260	19	22
β-strand	265-285	21	22
β-strand	290-292	3	22

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	25
β-strand	14	1	20
β-strand	21-29	9	21
β-strand	34-43	10	21
β-strand	48	1	26
β-strand	51-61	11	21
β-strand	66-70	5	27
β-strand	75-89	15	27
β-strand	97-102	6	21
α-helix	105-108	4
β-strand	109-127	19	6
β-strand	133-151	19	6
β-strand	153-158	6	27
β-strand	164-171	8	27
β-strand	174-176	3	28
β-strand	179-182	4	28
β-strand	188	1	27
β-strand	192	1	27
β-strand	197	1	29
α-helix	206-208	3
β-strand	210	1	29
α-helix	211-212	2
α-helix	213-215	3
β-strand	224	1	21
β-strand	228-234	7	21
β-strand	242-260	19	27
β-strand	265-285	21	27
β-strand	290-292	3	27

Chain F: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	30
β-strand	14	1	25
β-strand	21-29	9	26
β-strand	34-43	10	26
β-strand	48	1	31
β-strand	51-57	7	26
β-strand	60-61	2	26
β-strand	66-71	6	32
β-strand	75-89	15	32
β-strand	97-102	6	26
β-strand	109-121	13	6
β-strand	124-126	3	6
β-strand	132-151	20	6
β-strand	153-157	5	32
β-strand	164-171	8	32
β-strand	174-176	3	33
β-strand	179-182	4	33
β-strand	188	1	32
β-strand	192	1	32
β-strand	197	1	34
α-helix	206-208	3
β-strand	210	1	34
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	26
β-strand	228-234	7	26
β-strand	242-260	19	32
β-strand	265-285	21	32
β-strand	290-292	3	32

Chain G: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	2
β-strand	14	1	30
β-strand	21-29	9	31
β-strand	34-43	10	31
β-strand	48	1	3
β-strand	51-57	7	31
β-strand	60-61	2	31
β-strand	66-70	5	35
β-strand	75-89	15	35
β-strand	97-102	6	31
β-strand	109-121	13	6
β-strand	124-126	3	7
β-strand	132-134	3	7
β-strand	135-151	17	6
β-strand	153-158	6	35
β-strand	164-171	8	35
β-strand	174-176	3	36
β-strand	179-182	4	36
β-strand	188	1	35
β-strand	192	1	35
β-strand	197	1	37
α-helix	206-208	3
β-strand	210	1	37
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	31
β-strand	228-234	7	31
β-strand	242-260	19	35
β-strand	265-285	21	35
β-strand	290-292	3	35

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

>3M4E_1 Alpha-hemolysin (chains A, B, C, D, E, F, G)
ADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKGT
IAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYNSTLTYGF
NGNVTGDDTGKIGGLIGANVSIGHTLKYVQPDFKTILESPTDKKVGWKVIFNNMVNQNWG
PYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKASK
QQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTN

Primary citation

Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores. Banerjee, A., Mikhailova, E., Cheley, S. et al. Proc Natl Acad Sci U S A (2010) 107:8165-8170. DOI 10.1073/pnas.0914229107 · 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
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
9M4P 3.1 Å, Cryo-EM structure of alpha-hemolysin heptameric pore state in the presence of RBC

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