8JX2: Alpha hemolysin fused with spy-catcher

alpha-Hemolysin(G122S/K147R)-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: 32,872
Mol. weight: 586.65 kDa
Released: 3 Jul 2024

Explore 8JX2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JX2 contains 72 α-helices and 335 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: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	1
β-strand	14	1	2
β-strand	20-29	10	3
β-strand	34-43	10	3
β-strand	48	1	4
β-strand	51-61	11	3
β-strand	66-70	5	5
β-strand	75-89	15	5
β-strand	97-102	6	3
α-helix	105-108	4
β-strand	109-127	19	6
β-strand	134-151	18	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	188	1	5
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	242-259	18	5
β-strand	266-285	20	5
β-strand	290-292	3	5

Chain B: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	9
β-strand	14	1	1
β-strand	20-29	10	4
β-strand	34-43	10	4
β-strand	48	1	10
β-strand	51-61	11	4
β-strand	66-70	5	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	188	1	11
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	242-261	20	11
β-strand	264-285	22	11
β-strand	290-292	3	11

Chain C: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	14
β-strand	14	1	9
β-strand	20-29	10	10
β-strand	34-43	10	10
β-strand	48	1	15
β-strand	51-61	11	10
β-strand	66-69	4	16
β-strand	75-89	15	16
β-strand	97-102	6	10
β-strand	109-127	19	6
β-strand	133-151	19	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	188	1	16
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	228-234	7	10
β-strand	242-259	18	16
β-strand	266-285	20	16
β-strand	290-292	3	16

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	19
β-strand	14	1	14
β-strand	20-29	10	15
β-strand	34-43	10	15
β-strand	48	1	20
β-strand	51-61	11	15
β-strand	66-69	4	21
β-strand	75-89	15	21
β-strand	97-102	6	15
α-helix	105-108	4
β-strand	109-127	19	6
β-strand	132-151	20	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	188	1	21
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	242-259	18	21
β-strand	266-285	20	21
β-strand	290-292	3	21

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	24
β-strand	14	1	19
β-strand	20-29	10	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	109-127	19	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	188	1	26
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	242-259	18	26
β-strand	266-285	20	26
β-strand	290-292	3	26

Chain F: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	29
β-strand	14	1	24
β-strand	20-29	10	25
β-strand	34-43	10	25
β-strand	48	1	30
β-strand	51-61	11	25
β-strand	66-69	4	31
β-strand	75-89	15	31
β-strand	97-102	6	25
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	174-176	3	32
β-strand	179-182	4	32
β-strand	188	1	31
β-strand	192	1	31
β-strand	197	1	33
α-helix	206-208	3
β-strand	210	1	33
α-helix	211-212	2
α-helix	213-215	3
α-helix	218-221	4
β-strand	224	1	25
β-strand	228-234	7	25
β-strand	242-261	20	31
β-strand	264-285	22	31
β-strand	290-292	3	31

Chain G: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	7	1	2
β-strand	14	1	29
β-strand	20-29	10	30
β-strand	34-43	10	30
β-strand	48	1	3
β-strand	51-61	11	30
β-strand	66-69	4	34
β-strand	75-89	15	34
β-strand	97-102	6	30
α-helix	105-108	4
β-strand	109-126	18	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	188	1	34
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	242-259	18	34
β-strand	266-285	20	34
β-strand	290-292	3	34

Chain H: 5 helices, 23 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	66-71	6	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	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	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

3 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

>8JX2_1 alpha hemolysin fused with spy-catcher (chains A, B, C, D, E, F, G)
MADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKG
TIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYG
FNSNVTGDDTGKIGGLIGANVSIGHTLRYVQPDFKTILESPTDKKVGWKVIFNNMVNQNW
GPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKAS
KQQTNIDVIYERVRDDYQLHWTSTNWKGTNTKDKWTDRSSERYKIDWEKEEMTNGSSGSV
TTLSGLSGEQGPSGDMTTEEDSATHIKFSKRDEDGRELAGATMELRDSSGKTISTWISDG
HVKDFYLYPGKYTFVETAAPDGYEVATPIEFTVNEDGQVTVDGEATEGDAHTGGSHHHHH
H

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

>8JX2_2 alpha hemolysin fused with spy-tag (chains H, I, J, K, L, M, N)
MADSDINIKTGTTDIGSNTTVKTGDLVTYDKENGMHKKVFYSFIDDKNHNKKLLVIRTKG
TIAGQYRVYSEEGANKSGLAWPSAFKVQLQLPDNEVAQISDYYPRNSIDTKEYMSTLTYG
FNSNVTGDDTGKIGGLIGANVSIGHTLRYVQPDFKTILESPTDKKVGWKVIFNNMVNQNW
GPYDRDSWNPVYGNQLFMKTRNGSMKAADNFLDPNKASSLLSSGFSPDFATVITMDRKAS
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
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
9M4P 3.1 Å, Cryo-EM structure of alpha-hemolysin heptameric pore state in the presence of RBC

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