1FNV: Streptococcal pyrogenic exotoxin a

Name: PDB 1FNV: Structure of streptococcal pyrogenic exotoxin a
Published: 2000-11-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Structure of streptococcal pyrogenic exotoxin a. Determined by X-ray diffraction at 3.6 Å resolution. Released 17 Nov 2000.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Streptococcus pyogenes phage T12
Chains: 4
Atoms: 7,308
Mol. weight: 105.25 kDa
Ligands: CD
Released: 17 Nov 2000

Explore 1FNV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1FNV contains 25 α-helices and 84 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: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	19-26	8
α-helix	28-29	2
β-strand	30-35	6	1
β-strand	39	1	2
β-strand	47-48	2	2
β-strand	52	1	3
β-strand	55	1	3
β-strand	58-61	4	2
α-helix	65-71	7
β-strand	76-80	5	1
β-strand	83	1	2
β-strand	98-100	3	2
β-strand	103-105	3	1
β-strand	110	1	4
β-strand	117-123	7	5
β-strand	126-133	8	5
β-strand	137	1	4
β-strand	139-141	3	6
α-helix	142-155	14
β-strand	161	1	7
β-strand	163	1	7
β-strand	167-175	9	5
β-strand	182-185	4	5
α-helix	194-197	4
α-helix	198-201	4
β-strand	206-208	3	6
β-strand	213-220	8	5

Chain B: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	319-326	8
β-strand	330-335	6	8
β-strand	339	1	9
β-strand	345-348	4	9
β-strand	352	1	10
β-strand	355	1	10
β-strand	358-361	4	9
α-helix	365-371	7
β-strand	376-380	5	8
β-strand	382-383	2	9
β-strand	397-400	4	9
β-strand	403-405	3	8
β-strand	410	1	11
β-strand	417-423	7	12
β-strand	426-433	8	12
β-strand	437	1	11
β-strand	439-441	3	13
α-helix	442-455	14
β-strand	461	1	14
β-strand	463	1	14
β-strand	471-476	6	12
β-strand	482-485	4	12
α-helix	494-497	4
α-helix	498-501	4
β-strand	506-508	3	13
β-strand	512-518	7	12

Chain C: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	619-626	8
α-helix	628-629	2
β-strand	630-635	6	15
β-strand	639	1	16
β-strand	645-648	4	16
β-strand	652	1	17
β-strand	655	1	17
β-strand	658-661	4	16
α-helix	665-668	4
β-strand	676-680	5	15
β-strand	682-683	2	16
β-strand	697-700	4	16
β-strand	703-705	3	15
β-strand	710	1	18
β-strand	717-723	7	19
β-strand	726-733	8	19
β-strand	737	1	18
β-strand	739-741	3	20
α-helix	742-755	14
β-strand	761	1	21
β-strand	763	1	21
β-strand	769-775	7	19
β-strand	782-785	4	19
α-helix	794-797	4
α-helix	798-801	4
β-strand	806-808	3	20
β-strand	813-819	7	19

Chain D: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	918-921	4
α-helix	922-926	5
β-strand	930-935	6	22
β-strand	939	1	23
β-strand	945-948	4	23
β-strand	952	1	24
β-strand	955	1	24
β-strand	958-961	4	23
α-helix	965-971	7
β-strand	976-980	5	22
β-strand	983	1	23
β-strand	997-1000	4	23
β-strand	1003-1005	3	22
β-strand	1010	1	25
α-helix	1014-1016	3
β-strand	1017-1023	7	26
β-strand	1026-1033	8	26
β-strand	1037	1	25
β-strand	1039-1041	3	27
α-helix	1042-1055	14
β-strand	1061	1	28
β-strand	1063	1	28
β-strand	1069-1076	8	26
β-strand	1082-1085	4	26
α-helix	1094-1097	4
α-helix	1098-1102	5
β-strand	1106-1108	3	27
β-strand	1112-1119	8	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Exotoxin type A precursor (allele 1)	A, B, C, D	protein	221	Streptococcus pyogenes phage T12	P0DJY7 (AlphaFold model)

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

>1FNV_1 EXOTOXIN TYPE A PRECURSOR (ALLELE 1) (chains A, B, C, D)
QQDPDPSQLHRSSLVKNLQNIYFLYEGDPVTHENVKSVDQLLSHDLIYNVSGPNYDKLKT
ELKNQEMATLFKDKNVDIYGVEYYHLCYLCENAERSACIYGGVTNHEGNHLEIPKKIVVK
VSIDGIQSLSFDIETNKKMVTAQELDYKVRKYTIDNKQLYTNGPSKYETGYIKFIPKNKE
SFWFDFFPEPEFTQSKYLMIYKDNETLDNKTSQIEVYLTTK

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	16

Primary citation

Structure of streptococcal pyrogenic exotoxin A reveals a novel metal cluster. Earhart, C.A., Vath, G.M., Roggiani, M. et al. Protein Sci (2000) 9:1847-1851. PubMed

Other PDB entries of the same protein (UniProt P0DJY7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1L0Y 2.5 Å, T cell receptor beta chain complexed with superantigen SpeA soaked with zinc
1B1Z 2.57 Å, Streptococcal pyrogenic exotoxin A1
1UUP 2.6 Å, Crystal Structure of A Dimeric Form of Streptococcal Pyrogenic Exotoxin A (SpeA1).
1L0X 2.8 Å, TCR beta chain complexed with streptococcal superantigen SpeA
1HA5 2.82 Å, Structural features of a zinc-binding site in the superantigen streptococcal pyrogenic…
1FNW 3.9 Å, Crystal structure of streptococcal pyrogenic exotoxin a

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