SMTL ID : 9ash.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x ATP- A- A: RNA (5'-D(*(ATP))-R(P*AP*A)-3')(Non-covalent)

ATP-A-A.1: 31 residues within 4Å: Chain A: Y.304, Y.311, R.365, D.366, Y.368, R.369, S.372, D.520, V.521, D.522, N.523, L.524, G.525, F.528, I.529, T.542, S.546, M.549, S.550, G.575, D.576, K.636, K.649 Chain B: K.83, E.84, E.86, P.88, K.90, K.93 Ligands: MG.3, MG.4 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.523, A:L.524, A:G.525, A:Q.526, A:S.546, A:S.550 Salt bridges: A:K.636, A:K.649, B:K.93, B:K.93, B:K.93 pi-Stacking: A:Y.304, A:F.528

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

ATP.2: 18 residues within 4Å: Chain A: M.254, S.255, G.256, V.257, Q.258, I.261, Y.262, S.277, L.280, D.281, G.307, G.308, K.379, Y.572, G.575, D.577 Ligands: MG.3, MG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.256, A:V.257, A:Q.258, A:Q.258, A:S.277, A:D.281, A:Y.572, A:G.575 Salt bridges: A:K.379 pi-Stacking: A:Y.572, A:Y.572

3 x MG: MAGNESIUM ION(Non-covalent)

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
F

D
H

E
G

F
I

H
D

I
E

K
C

L
J

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

CRISPR-associated protein Csm4

CRISPR system Cms endoribonuclease Csm3

CRISPR system Cms protein Csm2

CRISPR system Cms protein Csm5

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