SMTL ID : 8ff4.1

Cryo-EM structure of Cascade-DNA-TniQ-TnsC complex (composite) in type I-B CAST system

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-6-1-3-1-7-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain Q: 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 Chain R: Q.220, R.223 Ligands: MG.2 18 PLIP interactions: 14 interactions with chain Q, 4 interactions with chain R Hydrogen bonds: Q:T.27, Q:V.28, Q:V.28, Q:G.60, Q:V.61, Q:G.62, Q:K.63, Q:T.64, Q:T.65, Q:T.65, Q:E.172, Q:K.282, R:Q.220, R:Q.220 Salt bridges: Q:K.63, Q:K.63, R:R.223, R:R.223 ATP.3: 21 residues within 4Å: Chain R: 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 S: Q.220, R.223, R.224 Ligands: MG.4 17 PLIP interactions: 12 interactions with chain R, 5 interactions with chain S Hydrogen bonds: R:V.28, R:V.28, R:A.58, R:G.60, R:V.61, R:G.62, R:K.63, R:T.64, R:T.65, R:K.282, S:Q.220 Salt bridges: R:K.63, R:K.63, S:R.223, S:R.223, S:R.223, S:R.224 ATP.5: 22 residues within 4Å: Chain S: 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 T: Q.220, R.223, R.224 Ligands: MG.6 19 PLIP interactions: 14 interactions with chain S, 5 interactions with chain T Hydrogen bonds: S:V.28, S:V.28, S:A.58, S:G.60, S:V.61, S:G.62, S:G.62, S:K.63, S:T.64, S:T.65, S:E.172, S:K.282, T:Q.220, T:R.223 Salt bridges: S:K.63, S:K.63, T:R.223, T:R.223, T:R.224 ATP.7: 20 residues within 4Å: Chain T: 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 U: Q.220, R.223, R.224 Ligands: MG.8 20 PLIP interactions: 14 interactions with chain T, 6 interactions with chain U Hydrogen bonds: T:V.28, T:V.28, T:A.58, T:G.60, T:V.61, T:G.62, T:G.62, T:K.63, T:T.64, T:T.65, T:E.172, T:K.282, U:Q.220, U:Q.220 Salt bridges: T:K.63, T:K.63, U:R.223, U:R.223, U:R.223, U:R.224 ATP.9: 21 residues within 4Å: Chain U: 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 V: Q.220, R.223, R.224 Ligands: MG.10 21 PLIP interactions: 16 interactions with chain U, 5 interactions with chain V Hydrogen bonds: U:T.27, U:V.28, U:V.28, U:A.58, U:S.59, U:G.60, U:V.61, U:G.62, U:G.62, U:K.63, U:T.64, U:T.65, U:K.282, U:K.286, V:Q.220 Salt bridges: U:K.63, U:K.63, V:R.223, V:R.223, V:R.223, V:R.224 ATP.11: 19 residues within 4Å: Chain V: 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 Chain W: Q.220, R.224 Ligands: MG.12 16 PLIP interactions: 12 interactions with chain V, 4 interactions with chain W Hydrogen bonds: V:V.28, V:V.28, V:A.58, V:G.60, V:V.61, V:K.63, V:T.64, V:T.65, V:E.172, V:K.282, W:Q.220, W:Q.220 Salt bridges: V:K.63, V:K.63, W:R.223, W:R.224 ATP.13: 17 residues within 4Å: Chain W: E.24, 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, K.282, K.286 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain W Hydrogen bonds: W:E.24, W:T.27, W:V.28, W:V.28, W:A.58, W:V.61, W:G.62, W:G.62, W:K.63, W:T.64, W:T.65, W:T.65, W:K.282 Salt bridges: W:K.63, W:K.63

7 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain Q: T.64 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:T.64 MG.4: 2 residues within 4Å: Chain R: T.64 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain R Metal complexes: R:T.64 MG.6: 2 residues within 4Å: Chain S: T.64 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain S Metal complexes: S:T.64 MG.8: 2 residues within 4Å: Chain T: T.64 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain T Metal complexes: T:T.64 MG.10: 2 residues within 4Å: Chain U: T.64 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain U Metal complexes: U:T.64 MG.12: 2 residues within 4Å: Chain V: T.64 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain V Metal complexes: V:T.64 MG.14: 2 residues within 4Å: Chain W: T.64 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain W Metal complexes: W: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

Type I-B CRISPR-associated protein Cas5: A
Type I-B CRISPR-associated protein Cas6: B
Type I-B CRISPR-associated protein Cas7: CDEFGH
Type I-B CRISPR-associated protein Cas8: I
Type I-B CRISPR-associated protein Cas11: JKL
TniQ: P
TnsC: QRSTUVW

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

Type I-B CRISPR-associated protein Cas5

Type I-B CRISPR-associated protein Cas6

Type I-B CRISPR-associated protein Cas7

Type I-B CRISPR-associated protein Cas8

Type I-B CRISPR-associated protein Cas11

TniQ

TnsC

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