4BIK: Intermedilysin

Structure of a disulfide locked mutant of Intermedilysin with human CD59. Determined by X-ray diffraction at 3.49 Å resolution. Released 8 May 2013.

Method: X-ray diffraction
Resolution: 3.49 Å
Organisms: STREPTOCOCCUS INTERMEDIUS, HOMO SAPIENS
Chains: 4
Atoms: 8,387
Mol. weight: 136.52 kDa
Released: 8 May 2013

Explore 4BIK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4BIK contains 48 α-helices and 62 β-strands across 4 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: 22 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	57-70	14
α-helix	75-78	4
β-strand	80-82	3	1
β-strand	90-97	8	1
β-strand	100-115	16	1
β-strand	118-119	2	2
α-helix	120	1
α-helix	125-127	3
β-strand	133-135	3	2
α-helix	138-141	4
α-helix	145-146	2
β-strand	147	1	2
α-helix	151	1
β-strand	152	1	3
α-helix	153-154	2
β-strand	155-159	5	2
β-strand	170-173	4	2
α-helix	178-194	17
α-helix	196-198	3
β-strand	205-212	8	2
α-helix	216-223	8
α-helix	227-230	4
α-helix	238-242	5
β-strand	247-262	16	2
α-helix	263-265	3
α-helix	268-271	4
β-strand	272	1	3
α-helix	278-283	6
β-strand	292-310	19	2
α-helix	318-325	8
α-helix	336-341	6
β-strand	343-349	7	2
β-strand	361-362	2	2
α-helix	366-374	9
α-helix	383-384	2
β-strand	385-393	9	2
α-helix	398	1
β-strand	399	1	2
α-helix	400	1
β-strand	402-417	16	1
β-strand	419-425	7	4
β-strand	432-443	12	5
β-strand	447-454	8	5
β-strand	466-472	7	4
β-strand	476-486	11	5
β-strand	494-503	10	5
β-strand	509-515	7	4
β-strand	520-522	3	4
β-strand	525-526	2	4

Chains B and D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	6
β-strand	16-18	3	6
β-strand	25-31	7	5
β-strand	34-40	7	5
α-helix	42-44	3
α-helix	47-54	8
β-strand	60-64	5	5
α-helix	72-74	3

Chain C: 20 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	58-70	13
β-strand	80-82	3	7
β-strand	90-97	8	7
β-strand	100-115	16	7
β-strand	118-119	2	8
α-helix	120	1
α-helix	125-127	3
β-strand	133-135	3	8
α-helix	138-141	4
α-helix	145-146	2
β-strand	147	1	8
α-helix	151-154	4
β-strand	155-159	5	8
α-helix	166-168	3
β-strand	170-173	4	8
α-helix	178-194	17
α-helix	196-198	3
β-strand	205-212	8	8
α-helix	216-223	8
α-helix	227-230	4
α-helix	238-242	5
β-strand	247-262	16	8
α-helix	263-265	3
α-helix	268-271	4
α-helix	278-283	6
β-strand	292-310	19	8
α-helix	318-325	8
α-helix	337-341	5
β-strand	344-349	6	8
α-helix	366-374	9
α-helix	383-384	2
β-strand	385-393	9	8
α-helix	398	1
β-strand	399-400	2	8
β-strand	402-417	16	7
β-strand	419-425	7	9
β-strand	431	1	10
β-strand	432-443	12	11
β-strand	447-454	8	11
β-strand	462	1	10
β-strand	466-472	7	9
β-strand	476-486	11	11
β-strand	494-503	10	11
β-strand	509-515	7	9
β-strand	520-526	7	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Intermedilysin	A, C	protein	535	STREPTOCOCCUS INTERMEDIUS	Q9LCB8 (AlphaFold model)
CD59 glycoprotein	B, D	protein	79	HOMO SAPIENS	P13987 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4BIK_1 INTERMEDILYSIN (chains A, C)
MGGSHHHHHHGMASMTGGQQMGRDLYDDDDKDRWGSETPTKPKAAQTEKKTEKKPENSNS
EAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATSK
LSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPS
NSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVD
FSSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSN
VSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKICAVVLGGNPGEA
SKVCTGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYK
DGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVR
NIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVKDNTD

Sequence of entity 2 (B, D), FASTA

>4BIK_2 CD59 GLYCOPROTEIN (chains B, D)
MLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENEL
TYYCCKKDLCNFNEQLENC

Primary citation

Structural Basis for Recognition of the Pore- Forming Toxin Intermedilysin by Human Complement Receptor Cd59. Johnson, S., Brooks, N.J., Smith, R.A.G. et al. Cell Rep (2013) 3:1369. DOI 10.1016/J.CELREP.2013.04.029 · 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
6ZD0 4.6 Å, Disulfide-locked early prepore intermedilysin-CD59

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