SMTL ID : 6o7e.1

Cryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with AMPPNP in type III-A CRISPR-Cas system

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-2-1-1-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.403, C.406, C.427, C.430 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.403, A:C.406, A:C.427, A:C.430 ZN.7: 4 residues within 4Å: Chain C: H.112, C.114, C.123, C.126 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.112, C:C.114, C:C.123, C:C.126 ZN.8: 4 residues within 4Å: Chain D: H.112, C.114, C.123, C.126 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.112, D:C.114, D:C.123, D:C.126

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 19 residues within 4Å: Chain A: F.304, A.306, H.309, V.536, D.537, R.538, L.539, G.540, F.543, S.556, D.560, G.601, D.602, K.662, R.666 Chain E: Y.90, K.94 Ligands: MN.4, MN.5 11 PLIP interactions: 5 interactions with chain E, 6 interactions with chain A Hydrogen bonds: E:Y.90, E:Y.90, E:Y.90, E:K.94, A:D.535, A:R.538, A:L.539, A:G.540, A:G.601, A:K.662 Salt bridges: E:K.94 ANP.3: 18 residues within 4Å: Chain A: D.253, F.254, S.255, G.256, I.257, Q.258, I.261, S.277, L.280, G.307, G.308, K.381, Y.598, G.600, D.602, D.603 Ligands: MN.4, MN.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.253, A:G.256, A:I.257, A:Q.258, A:Q.258, A:S.277, A:D.602 pi-Stacking: A:Y.598, A:Y.598

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 5 residues within 4Å: Chain A: D.535, D.602 Ligands: ANP.2, ANP.3, MN.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.602, A:D.602 MN.5: 5 residues within 4Å: Chain A: D.535, V.536, D.602 Ligands: ANP.2, MN.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:V.536, A:D.602 MN.6: 3 residues within 4Å: Chain A: D.253, F.254 Ligands: ANP.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.253, A:D.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jia, N. et al., Second Messenger cA4Formation within the Composite Csm1 Palm Pocket of Type III-A CRISPR-Cas Csm Complex and Its Release Path. Mol.Cell (2019)

Release Date

2019-07-31

Peptides

Csm1: A
Csm2: B
Csm3: CD
Csm4: E
Csm5: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

H
Y

Csm1

Csm2

Csm3

Csm4

Csm5

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