SMTL ID : 8fcw.1

Cryo-EM structure of TnsC-DNA complex in type I-B CAST system

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-pentamer

Ligands

5 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: Y.26, T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, I.278, G.279, K.282, D.283 Chain B: Q.220, R.223, R.224 Ligands: MG.2 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:V.28, A:V.28, A:A.58, A:G.60, A:V.61, A:G.62, A:K.63, A:T.64, A:T.65, A:K.282, B:Q.220 Salt bridges: A:K.63, A:K.63, B:R.223, B:R.223, B:R.223, B:R.224 ATP.3: 22 residues within 4Å: Chain B: Y.26, T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, E.172, I.278, G.279, K.282, D.283 Chain C: Q.220, R.223, R.224 Ligands: MG.4 19 PLIP interactions: 14 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:V.28, B:V.28, B:A.58, B:G.60, B:V.61, B:G.62, B:G.62, B:K.63, B:T.64, B:T.65, B:E.172, B:K.282, C:Q.220, C:R.223 Salt bridges: B:K.63, B:K.63, C:R.223, C:R.223, C:R.224 ATP.5: 20 residues within 4Å: Chain C: Y.26, T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, E.172, G.279, K.282 Chain D: Q.220, R.223, R.224 Ligands: MG.6 22 PLIP interactions: 16 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:T.27, C:V.28, C:V.28, C:A.58, C:G.60, C:V.61, C:G.62, C:G.62, C:K.63, C:T.64, C:T.65, C:T.65, C:E.172, C:K.282, D:Q.220, D:Q.220 Salt bridges: C:K.63, C:K.63, D:R.223, D:R.223, D:R.223, D:R.224 ATP.7: 21 residues within 4Å: Chain D: Y.26, T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, I.278, G.279, K.282, K.286 Chain E: Q.220, R.223, R.224 Ligands: MG.8 21 PLIP interactions: 16 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:T.27, D:V.28, D:V.28, D:A.58, D:G.60, D:V.61, D:G.62, D:G.62, D:K.63, D:T.64, D:T.65, D:T.65, D:K.282, D:K.286, E:Q.220 Salt bridges: D:K.63, D:K.63, E:R.223, E:R.223, E:R.223, E:R.224 ATP.9: 17 residues within 4Å: Chain E: T.27, V.28, H.30, L.33, A.58, S.59, G.60, V.61, G.62, K.63, T.64, T.65, E.172, I.278, G.279, K.282 Ligands: MG.10 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:V.28, E:V.28, E:A.58, E:G.60, E:G.62, E:K.63, E:T.64, E:T.65, E:E.172, E:K.282 Salt bridges: E:K.63, E:K.63

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.64 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.64 MG.4: 2 residues within 4Å: Chain B: T.64 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.64 MG.6: 2 residues within 4Å: Chain C: T.64 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.64 MG.8: 2 residues within 4Å: Chain D: T.64 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.64 MG.10: 2 residues within 4Å: Chain E: T.64 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., Molecular mechanism for Tn7-like transposon recruitment by a type I-B CRISPR effector. Cell (2023)

Release Date

2023-08-09

Peptides

TnsC: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
S

C
T

D
U

E
V

TnsC

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