SMTL ID : 9asi.1

Cryo-EM structure of the active Lactococcus lactis Csm bound to target in pre-cleavage stage

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-4-3-1-1-mer

Ligands

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

ATP.1: 18 residues within 4Å: Chain L: M.254, S.255, G.256, V.257, Q.258, I.261, S.277, L.280, D.281, G.307, G.308, K.379, R.382, Y.572, G.575, D.577 Ligands: MG.2, MG.4 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:G.256, L:V.257, L:Q.258, L:Q.258, L:S.277, L:D.281, L:G.307, L:R.382, L:Y.572 Salt bridges: L:K.379, L:K.379 pi-Stacking: L:Y.572 ATP.5: 20 residues within 4Å: Chain A: K.90 Chain L: Y.304, H.309, D.520, V.521, D.522, N.523, L.524, G.525, F.528, S.546, M.549, S.550, G.575, D.576, K.636, K.649 Ligands: MG.2, MG.3, AMP.6 15 PLIP interactions: 13 interactions with chain L, 2 interactions with chain A Hydrogen bonds: L:D.520, L:V.521, L:D.522, L:D.522, L:N.523, L:L.524, L:G.525, L:S.546 Salt bridges: L:K.636, L:K.636, L:K.649, L:K.649, A:K.90, A:K.90 pi-Stacking: L:Y.304

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain L: D.520, D.577 Ligands: ATP.1, MG.3, ATP.5 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.577 MG.3: 5 residues within 4Å: Chain L: D.520, V.521, D.576 Ligands: MG.2, ATP.5 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.520, L:V.521, L:D.576, L:D.576 MG.4: 3 residues within 4Å: Chain L: D.253, M.254 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.253

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 8 residues within 4Å: Chain L: H.309, Y.311, Y.368, S.372, G.525, F.528, T.542 Ligands: ATP.5 6 PLIP interactions: 6 interactions with chain L Hydrogen bonds: L:Y.311, L:Y.368, L:S.372 Salt bridges: L:H.309 pi-Stacking: L:Y.368, L:F.528

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goswami, H.N. et al., Molecular basis for cA6 synthesis by a type III-A CRISPR-Cas enzyme and its conversion to cA4 production. Nucleic Acids Res. (2024)

Release Date

2024-08-14

Peptides

CRISPR-associated protein Csm4: A
CRISPR system Cms endoribonuclease Csm3: BCDE
CRISPR system Cms protein Csm2: GHJ
CRISPR system Cms protein Csm5: K
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A): L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
F

C
H

D
G

E
I

G
D

H
E

J
C

K
J

L
A

CRISPR-associated protein Csm4

CRISPR system Cms endoribonuclease Csm3

CRISPR system Cms protein Csm2

CRISPR system Cms protein Csm5

CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)

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