8JX3: Alpha hemolysin fused with spy-catcher

alpha-Hemolysin(G122S/K147R/K237C)-SpyTag/SpyCatcher head to head 14-mer. Determined by electron microscopy at 2.2 Å resolution. Released 3 Jul 2024.

Method: Electron microscopy
Resolution: 2.2 Å
Organism: Staphylococcus aureus
Chains: 14
Atoms: 32,826
Mol. weight: 586.29 kDa
Released: 3 Jul 2024

Explore 8JX3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JX3 contains 77 α-helices and 325 β-strands across 14 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: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
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	66-71	6	5
β-strand	75-89	15	5
β-strand	97-102	6	3
β-strand	109-126	18	6
β-strand	132-151	20	6
β-strand	153-158	6	5
β-strand	164-171	8	5
β-strand	174-176	3	7
β-strand	179-182	4	7
β-strand	192	1	5
β-strand	197	1	8
α-helix	206-208	3
β-strand	210	1	8
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: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	9
β-strand	14	1	1
β-strand	21-29	9	4
β-strand	34-43	10	4
β-strand	48	1	10
β-strand	51-61	11	4
β-strand	66-71	6	11
β-strand	75-89	15	11
β-strand	97-102	6	4
β-strand	109-127	19	6
β-strand	133-151	19	6
β-strand	153-158	6	11
β-strand	164-171	8	11
β-strand	174-176	3	12
β-strand	179-182	4	12
β-strand	192	1	11
β-strand	197	1	13
α-helix	206-208	3
β-strand	210	1	13
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	11
β-strand	265-285	21	11
β-strand	290-292	3	11

Chain C: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	14
β-strand	14	1	9
β-strand	21-29	9	10
β-strand	34-43	10	10
β-strand	48	1	15
β-strand	51-61	11	10
β-strand	66-71	6	16
β-strand	75-89	15	16
β-strand	97-102	6	10
α-helix	105-108	4
β-strand	109-127	19	6
β-strand	132-151	20	6
β-strand	153-158	6	16
β-strand	164-171	8	16
β-strand	174-176	3	17
β-strand	179-182	4	17
β-strand	192	1	16
β-strand	197	1	18
α-helix	206-208	3
β-strand	210	1	18
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	10
β-strand	227-234	8	10
β-strand	242-260	19	16
β-strand	265-285	21	16
β-strand	290-292	3	16

Chains D and F: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	19
β-strand	14	1	14
β-strand	21-29	9	15
β-strand	34-43	10	15
β-strand	48	1	20
β-strand	51-61	11	15
β-strand	66-71	6	21
β-strand	75-89	15	21
β-strand	97-102	6	15
α-helix	105-108	4
β-strand	109-126	18	6
β-strand	133-151	19	6
β-strand	153-158	6	21
β-strand	164-171	8	21
β-strand	174-176	3	22
β-strand	179-182	4	22
β-strand	192	1	21
β-strand	197	1	23
α-helix	206-208	3
β-strand	210	1	23
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	15
β-strand	228-234	7	15
β-strand	242-260	19	21
β-strand	265-285	21	21
β-strand	290-292	3	21

Chain E: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	7	1	24
β-strand	14	1	19
β-strand	21-29	9	20
β-strand	34-43	10	20
β-strand	48	1	25
β-strand	51-61	11	20
β-strand	66-71	6	26
β-strand	75-89	15	26
β-strand	97-102	6	20
β-strand	109-126	18	6
β-strand	133-151	19	6
β-strand	153-158	6	26
β-strand	164-171	8	26
β-strand	174-176	3	27
β-strand	179-182	4	27
β-strand	192	1	26
β-strand	197	1	28
α-helix	206-208	3
β-strand	210	1	28
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	20
β-strand	228-234	7	20
β-strand	242-260	19	26
β-strand	265-285	21	26
β-strand	290-292	3	26

Chain G: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	2
β-strand	14	1	29
β-strand	21-29	9	30
β-strand	34-43	10	30
β-strand	48	1	3
β-strand	51-61	11	30
β-strand	66-71	6	34
β-strand	75-89	15	34
β-strand	97-102	6	30
α-helix	105-108	4
β-strand	109-127	19	6
β-strand	133-151	19	6
β-strand	153-158	6	34
β-strand	164-171	8	34
β-strand	174-176	3	35
β-strand	179-182	4	35
β-strand	192	1	34
β-strand	197	1	36
α-helix	206-208	3
β-strand	210	1	36
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	30
β-strand	228-234	7	30
β-strand	242-260	19	34
β-strand	265-285	21	34
β-strand	290-292	3	34

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	37
β-strand	14	1	38
β-strand	20-29	10	39
β-strand	34-43	10	39
β-strand	48	1	40
β-strand	51-61	11	39
β-strand	66-70	5	41
β-strand	75-89	15	41
β-strand	97-102	6	39
α-helix	105-108	4
β-strand	109-127	19	42
β-strand	132-151	20	42
β-strand	153-158	6	41
β-strand	164-171	8	41
β-strand	174-176	3	43
β-strand	179-182	4	43
β-strand	188	1	41
β-strand	192	1	41
β-strand	197	1	44
α-helix	206-208	3
β-strand	210	1	44
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	39
β-strand	228-234	7	39
β-strand	242-260	19	41
β-strand	265-285	21	41
β-strand	290-292	3	41

Chain I: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	45
β-strand	14	1	37
β-strand	21-29	9	40
β-strand	34-43	10	40
β-strand	48	1	46
β-strand	51-61	11	40
β-strand	66-71	6	47
β-strand	75-89	15	47
β-strand	97-102	6	40
β-strand	109-127	19	42
β-strand	133-151	19	42
β-strand	153-158	6	47
β-strand	164-171	8	47
β-strand	174-176	3	48
β-strand	179-182	4	48
β-strand	192	1	47
β-strand	197	1	49
α-helix	206-208	3
β-strand	210	1	49
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	40
β-strand	228-234	7	40
β-strand	242-260	19	47
β-strand	265-285	21	47
β-strand	290-292	3	47

5 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
alpha hemolysin fused with spy-catcher	A, B, C, D, E, F, G	protein	421	Staphylococcus aureus	P09616 (AlphaFold model)
alpha hemolysin fused with spy-tag	H, I, J, K, L, M, N	protein	324	Staphylococcus aureus	P09616 (AlphaFold model)

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

>8JX3_1 alpha hemolysin fused with spy-catcher (chains A, B, C, D, E, F, G)
MADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKG
TIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYG
FNSNVTGDDTGKIGGLIGANVSIGHTLRYVQPDFKTILESPTDKKVGWKVIFNNMVNQNW
GPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRCAS
KQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTNGSSGSV
TTLSGLSGEQGPSGDMTTEEDSATHIKFSKRDEDGRELAGATMELRDSSGKTISTWISDG
HVKDFYLYPGKYTFVETAAPDGYEVATPIEFTVNEDGQVTVDGEATEGDAHTGGSHHHHH
H

Sequence of entity 2 (H, I, J, K, L, M, N), FASTA

>8JX3_2 alpha hemolysin fused with spy-tag (chains H, I, J, K, L, M, N)
MADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKG
TIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYG
FNSNVTGDDTGKIGGLIGANVSIGHTLRYVQPDFKTILESPTDKKVGWKVIFNNMVNQNW
GPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRCAS
KQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTNGSSGSR
GVPHIVMVDAYKRYKGGSHHHHHH

Primary citation

alpha-Hemolysin(G122S/K147R)-SpyTag/SpyCatcher head to head 14-mer. Ishii, Y., Naito, K., Yokoyama, T. et al. To be published.

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
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
9M4P 3.1 Å, Cryo-EM structure of alpha-hemolysin heptameric pore state in the presence of RBC

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