SMTL ID : 6ut5.1

Cryo-EM structure of the Thermococcus gammatolerans McrBC complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

5 x GSP: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE(Non-covalent)

GSP.1: 16 residues within 4Å: Chain A: N.193, P.217, G.218, T.219, G.220, K.221, T.222, W.223, E.357, F.438, I.447, H.501, S.502, L.505 Chain B: R.425 Ligands: MG.2 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.193, A:G.218, A:T.219, A:T.219, A:G.220, A:K.221, A:K.221, A:K.221, A:T.222, A:W.223, A:E.357, A:S.502 Water bridges: A:K.221, A:T.222, A:T.222 Salt bridges: A:K.221 pi-Stacking: A:W.223, A:W.223, A:W.223, A:W.223 pi-Cation interactions: A:W.223 GSP.3: 22 residues within 4Å: Chain B: P.217, G.218, T.219, G.220, K.221, T.222, W.223, E.357, F.438, I.447, K.451, H.501, S.502, L.505 Chain C: E.375, D.377, K.378, N.384, A.422, R.425, R.426 Ligands: MG.4 23 PLIP interactions: 16 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:G.218, B:T.219, B:T.219, B:G.220, B:K.221, B:K.221, B:K.221, B:T.222, B:W.223, B:K.451, B:K.451, C:K.378, C:N.384, C:R.425, C:R.426 Water bridges: B:T.222 Salt bridges: B:K.221, C:K.378, C:R.425, C:R.425 pi-Stacking: B:W.223, B:W.223 pi-Cation interactions: B:W.223 GSP.5: 22 residues within 4Å: Chain C: I.194, P.217, G.218, T.219, G.220, K.221, T.222, W.223, E.357, F.438, I.447, H.501, S.502, L.505 Chain D: E.375, D.377, K.378, N.384, A.422, R.425, R.426 Ligands: MG.6 27 PLIP interactions: 11 interactions with chain D, 16 interactions with chain C Hydrogen bonds: D:E.375, D:D.377, D:K.378, D:N.384, D:N.384, D:R.425, D:R.426, D:R.426, C:G.218, C:T.219, C:T.219, C:G.220, C:K.221, C:K.221, C:K.221, C:T.222, C:T.222, C:T.222, C:W.223 Salt bridges: D:K.378, D:R.425, D:R.425, C:K.221 pi-Stacking: C:W.223, C:W.223, C:W.223 pi-Cation interactions: C:W.223 GSP.7: 24 residues within 4Å: Chain D: N.193, P.216, P.217, G.218, T.219, G.220, K.221, T.222, W.223, E.357, N.410, F.438, I.447, H.501, S.502, L.505 Chain E: E.375, D.377, K.378, N.384, A.422, R.425, R.426 Ligands: MG.8 27 PLIP interactions: 16 interactions with chain D, 11 interactions with chain E Hydrogen bonds: D:N.193, D:N.193, D:P.216, D:G.218, D:T.219, D:G.220, D:K.221, D:T.222, D:T.222, D:W.223, E:D.377, E:K.378, E:K.378, E:N.384, E:R.425, E:R.426, E:R.426 Water bridges: D:T.222, E:E.375 Salt bridges: D:K.221, E:K.378, E:R.425, E:R.425 pi-Stacking: D:W.223, D:W.223, D:W.223 pi-Cation interactions: D:W.223 GSP.9: 24 residues within 4Å: Chain E: N.193, P.217, G.218, T.219, G.220, K.221, T.222, W.223, E.357, N.410, F.438, I.447, K.450, H.501, S.502, L.505 Chain F: E.375, D.377, K.378, N.384, A.422, R.425, R.426 Ligands: MG.10 23 PLIP interactions: 8 interactions with chain F, 15 interactions with chain E Hydrogen bonds: F:D.377, F:N.384, F:R.425, F:R.426, F:R.426, E:N.193, E:G.218, E:T.219, E:T.219, E:G.220, E:K.221, E:T.222, E:T.222, E:W.223, E:K.450, E:K.450 Salt bridges: F:K.378, F:R.425, F:R.425, E:K.221 pi-Stacking: E:W.223, E:W.223 pi-Cation interactions: E:W.223

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.222, D.356, E.357, T.408 Ligands: GSP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.222, A:D.356, H2O.1, H2O.1 MG.4: 5 residues within 4Å: Chain B: T.222, D.356, E.357, T.408 Ligands: GSP.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.222, B:D.356, H2O.1, H2O.1 MG.6: 5 residues within 4Å: Chain C: T.222, D.356, E.357 Chain D: R.426 Ligands: GSP.5 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.222, C:D.356, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain D: T.222, D.356, E.357, T.408 Ligands: GSP.7 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:T.222, H2O.1, H2O.1, H2O.1 MG.10: 5 residues within 4Å: Chain E: T.222, D.356, E.357 Chain F: R.426 Ligands: GSP.9 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.222, H2O.1, H2O.1, H2O.1 MG.12: 4 residues within 4Å: Chain F: T.222, D.356, E.357 Ligands: GDP.11 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:T.222, H2O.2, H2O.2

1 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.11: 17 residues within 4Å: Chain A: D.377, N.384 Chain F: P.217, G.218, T.219, G.220, K.221, T.222, W.223, N.410, F.438, I.447, K.450, H.501, S.502, L.505 Ligands: MG.12 20 PLIP interactions: 17 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:G.218, F:T.219, F:T.219, F:G.220, F:K.221, F:T.222, F:W.223, F:N.410, F:K.450, F:K.450, F:S.502, A:D.377, A:N.384 Water bridges: F:T.222, A:E.375 Salt bridges: F:K.221 pi-Stacking: F:W.223, F:W.223, F:W.223 pi-Cation interactions: F:W.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, Y. et al., Structural asymmetry governs the assembly and GTPase activity of McrBC restriction complexes. Nat Commun (2020)

Release Date

2020-10-21

Peptides

GTPase subunit of restriction endonuclease: ABCDEF
McrBC 5-methylcytosine restriction system component: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

GTPase subunit of restriction endonuclease

McrBC 5-methylcytosine restriction system component

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