6ZD0: Thiol-activated cytolysin

Disulfide-locked early prepore intermedilysin-CD59. Determined by electron microscopy at 4.6 Å resolution. Released 18 Nov 2020.

Method: Electron microscopy
Resolution: 4.6 Å
Organisms: Streptococcus intermedius, Homo sapiens
Chains: 6
Atoms: 7,962
Mol. weight: 204.92 kDa
Released: 18 Nov 2020

Explore 6ZD0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZD0 contains 58 α-helices and 98 β-strands across 6 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: 19 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	57-68	12
α-helix	75-78	4
β-strand	81-84	4	1
β-strand	91-97	7	1
β-strand	100-112	13	1
β-strand	115	1	2
β-strand	118-119	2	3
α-helix	122-124	3
β-strand	133-135	3	3
α-helix	138-141	4
α-helix	150-151	2
β-strand	152	1	4
β-strand	155-160	6	3
β-strand	170-173	4	3
α-helix	178-195	18
α-helix	197-199	3
β-strand	208-212	5	3
α-helix	216-223	8
α-helix	227-230	4
α-helix	232-234	3
α-helix	238-242	5
β-strand	247-262	16	3
α-helix	268-270	3
β-strand	272	1	4
α-helix	278-283	6
β-strand	292-310	19	3
α-helix	316-324	9
α-helix	336-341	6
β-strand	348	1	3
α-helix	359-362	4
α-helix	365-371	7
α-helix	379	1
β-strand	385-393	9	3
β-strand	398-399	2	3
α-helix	400	1
β-strand	402	1	2
β-strand	404-411	8	1
β-strand	414-417	4	1
β-strand	420-425	6	5
β-strand	431-442	12	6
β-strand	448-453	6	6
β-strand	467-470	4	5
β-strand	476-486	11	6
β-strand	494-503	10	6
β-strand	508-515	8	5
β-strand	520-525	6	5

Chain B: 1 helix, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	7
β-strand	16-18	3	7
β-strand	23	1	6
β-strand	25-31	7	6
β-strand	34-40	7	6
α-helix	47-53	7
β-strand	60-64	5	6

Chain C: 17 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	57-70	14
α-helix	75-78	4
β-strand	80-82	3	8
β-strand	90-97	8	9
β-strand	100-107	8	9
β-strand	108-111	4	10
β-strand	115	1	11
β-strand	118-119	2	12
α-helix	122-127	6
β-strand	133-135	3	12
α-helix	138-141	4
β-strand	155-159	5	12
β-strand	170-173	4	12
α-helix	178-195	18
α-helix	197-199	3
β-strand	208-212	5	12
α-helix	216-223	8
α-helix	227-230	4
α-helix	232-234	3
α-helix	238-242	5
β-strand	247-262	16	12
α-helix	268-271	4
α-helix	278-283	6
β-strand	292-310	19	12
α-helix	316-324	9
α-helix	336-341	6
β-strand	348	1	12
α-helix	358-362	5
α-helix	367-370	4
α-helix	371-376	6
β-strand	385	1	12
β-strand	388-393	6	12
β-strand	399	1	12
β-strand	402	1	11
β-strand	403-405	3	8
β-strand	406-409	4	10
β-strand	415-417	3	9
β-strand	420-423	4	13
β-strand	431-443	13	14
β-strand	447-453	7	14
β-strand	468-470	3	13
β-strand	476-485	10	14
β-strand	496-503	8	14
β-strand	508-516	9	13
β-strand	519-525	7	13

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	15
β-strand	16-18	3	15
β-strand	25-31	7	14
β-strand	34-40	7	14
α-helix	47-53	7
β-strand	60-64	5	14
α-helix	72-74	3

Chain E: 16 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	57-70	14
α-helix	75-78	4
β-strand	81-82	2	16
β-strand	91-97	7	16
β-strand	100-113	14	16
β-strand	118-119	2	17
α-helix	122-127	6
β-strand	134-135	2	17
α-helix	138-141	4
β-strand	152	1	18
β-strand	155-160	6	17
β-strand	170-173	4	17
α-helix	178-195	18
α-helix	197-199	3
β-strand	209-212	4	17
α-helix	217-221	5
α-helix	227-230	4
α-helix	238-242	5
β-strand	247-262	16	17
β-strand	272	1	18
α-helix	278-283	6
β-strand	292-310	19	17
α-helix	317-323	7
α-helix	336-341	6
β-strand	346-348	3	17
α-helix	357-362	6
α-helix	367-373	7
β-strand	386-393	8	17
α-helix	398	1
β-strand	399	1	17
α-helix	400	1
β-strand	404-413	10	16
β-strand	416	1	16
β-strand	419-425	7	19
β-strand	432-441	10	20
β-strand	449-454	6	20
β-strand	460-461	2	20
β-strand	466-472	7	19
β-strand	476-486	11	20
β-strand	494-503	10	20
β-strand	509-516	8	19
β-strand	519-526	8	19

Chain F: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	21
β-strand	8	1	20
β-strand	16-18	3	21
β-strand	25-31	7	20
β-strand	34-40	7	20
α-helix	42-44	3
α-helix	47-54	8
β-strand	60-64	5	20
α-helix	72-74	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Thiol-activated cytolysin	A, C, E	protein	535	Streptococcus intermedius	Q9LCB8 (AlphaFold model)
CD59 glycoprotein	B, D, F	protein	79	Homo sapiens	P13987 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>6ZD0_1 Thiol-activated cytolysin (chains A, C, E)
MGGSHHHHHHGMASMTGGQQMGRDLYDDDDKDRWGSETPTKPKAAQTEKKTEKKPENSNS
EAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVCEKKKQSISNATSK
LSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPS
NSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVD
FSSVHKCEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSN
VSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKITAVVLGGNPGEA
SKVITGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYK
DGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVR
NIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVKDNTD

Sequence of entity 2 (B, D, F), FASTA

>6ZD0_2 CD59 glycoprotein (chains B, D, F)
MLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENEL
TYYCCKKDLCNFNEQLENC

Primary citation

Structural basis for tuning activity and membrane specificity of bacterial cytolysins. Shah, N.R., Voisin, T.B., Parsons, E.S. et al. Nat Commun (2020) 11:5818-5818. DOI 10.1038/s41467-020-19482-6 · PubMed

Other PDB entries of the same protein (UniProt Q9LCB8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1S3R 2.6 Å, Crystal structure of the human-specific toxin intermedilysin
5IMT 2.7 Å, Toxin receptor complex
5IMW 2.89 Å, Trapped Toxin
4BIK 3.49 Å, Structure of a disulfide locked mutant of Intermedilysin with human CD59

Browse structure collections

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