SMTL ID : 6klo.1

Complex structure of Iota toxin enzymatic component (Ia) and binding component (Ib) pore with short stem

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-7-1-mer

Ligands

14 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: D.12, D.14, E.21, S.50, E.53, D.63 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.12, A:D.14, A:S.50, A:E.53, A:D.63 CA.2: 6 residues within 4Å: Chain A: D.10, D.12, D.14, I.16, E.21 Ligands: CA.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.10, A:D.12, A:D.14, A:I.16, A:E.21 CA.3: 7 residues within 4Å: Chain B: D.12, D.14, E.21, S.49, S.50, E.53, D.63 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.14, B:E.21, B:S.50, B:E.53, B:D.63 CA.4: 7 residues within 4Å: Chain B: D.10, D.12, D.14, I.16, P.17, D.18, E.21 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.10, B:D.12, B:D.14, B:I.16, B:E.21 CA.5: 7 residues within 4Å: Chain C: D.12, D.14, E.21, S.49, S.50, E.53, D.63 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.14, C:E.21, C:S.50, C:E.53, C:D.63 CA.6: 6 residues within 4Å: Chain C: D.10, D.12, D.14, I.16, D.18, E.21 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.10, C:D.12, C:D.14, C:I.16, C:E.21 CA.7: 6 residues within 4Å: Chain D: D.12, D.14, E.21, S.50, E.53, D.63 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.12, D:D.14, D:E.21, D:S.50, D:D.63 CA.8: 5 residues within 4Å: Chain D: D.10, D.12, D.14, I.16, E.21 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.10, D:D.12, D:D.14, D:I.16, D:E.21 CA.9: 6 residues within 4Å: Chain E: D.12, D.14, E.21, S.50, E.53, D.63 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.14, E:E.21, E:S.50, E:E.53, E:D.63 CA.10: 5 residues within 4Å: Chain E: D.10, D.12, D.14, I.16, E.21 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:D.10, E:D.12, E:D.14, E:I.16, E:E.21 CA.11: 6 residues within 4Å: Chain F: D.12, D.14, E.21, S.50, E.53, D.63 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.12, F:D.14, F:E.21, F:S.50, F:D.63 CA.12: 6 residues within 4Å: Chain F: D.10, D.12, D.14, I.16, D.18, E.21 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:D.10, F:D.12, F:D.14, F:I.16, F:E.21 CA.13: 6 residues within 4Å: Chain G: D.12, D.14, E.21, S.50, E.53, D.63 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.14, G:E.21, G:S.50, G:E.53, G:D.63 CA.14: 6 residues within 4Å: Chain G: D.10, D.12, D.14, I.16, D.18, E.21 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:D.10, G:D.12, G:D.14, G:I.16, G:E.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamada, T. et al., Cryo-EM structures reveal translocational unfolding in the clostridial binary iota toxin complex. Nat.Struct.Mol.Biol. (2020)

Release Date

2020-01-15

Peptides

Iota toxin component Ib: ABCDEFG
Iota toxin component Ia: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Iota toxin component Ib

Iota toxin component Ia

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