SMTL ID : 6ut4.1

Cryo-EM structure of the asymmetric AAA+ domain hexamer from Thermococcus gammatolerans McrB

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

GSP.1: 16 residues within 4Å: Chain A: P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, N.225, F.253, I.262, H.316, S.317, L.320 Chain B: R.240 Ligands: MG.2 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.33, A:K.36, A:K.36, A:K.36, A:T.37, A:W.38, A:S.317, B:R.240 Salt bridges: A:K.36 pi-Stacking: A:W.38, A:W.38, A:W.38 pi-Cation interactions: A:W.38 GSP.3: 20 residues within 4Å: Chain B: P.32, G.33, T.34, K.36, T.37, W.38, E.172, F.253, I.262, H.316, S.317, L.320 Chain C: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.4 22 PLIP interactions: 13 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:G.33, B:K.36, B:T.37, B:W.38, B:I.262, C:K.193, C:K.193, C:N.199, C:R.240, C:R.241, C:R.241 Water bridges: B:G.35, B:T.37, B:D.171, B:T.223 Salt bridges: B:K.36, C:K.193, C:R.240, C:R.240 pi-Stacking: B:W.38, B:W.38 pi-Cation interactions: B:W.38 GSP.5: 22 residues within 4Å: Chain C: P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, N.225, F.253, I.262, H.316, S.317, L.320 Chain D: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.6 24 PLIP interactions: 11 interactions with chain D, 13 interactions with chain C Hydrogen bonds: D:E.190, D:N.199, D:N.199, D:R.241, D:R.241, C:G.33, C:K.36, C:K.36, C:K.36, C:T.37, C:T.37, C:W.38 Water bridges: D:E.190, D:R.240, C:G.35 Salt bridges: D:K.193, D:K.193, D:R.240, D:R.240, C:K.36 pi-Stacking: C:W.38, C:W.38, C:W.38 pi-Cation interactions: C:W.38 GSP.7: 21 residues within 4Å: Chain D: P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, F.253, I.262, H.316, S.317, L.320 Chain E: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.8 26 PLIP interactions: 9 interactions with chain E, 17 interactions with chain D Hydrogen bonds: E:E.190, E:N.199, E:R.241, E:R.241, D:G.33, D:G.35, D:K.36, D:K.36, D:K.36, D:T.37, D:T.37, D:T.37, D:W.38 Water bridges: E:E.190, D:D.171, D:E.172, D:E.172 Salt bridges: E:K.193, E:K.193, E:R.240, E:R.240, D:K.36 pi-Stacking: D:W.38, D:W.38, D:W.38 pi-Cation interactions: D:W.38 GSP.9: 21 residues within 4Å: Chain E: P.32, G.33, T.34, G.35, K.36, T.37, W.38, E.172, F.253, I.262, H.316, S.317, L.320 Chain F: E.190, D.192, K.193, N.199, A.237, R.240, R.241 Ligands: MG.10 26 PLIP interactions: 10 interactions with chain F, 16 interactions with chain E Hydrogen bonds: F:E.190, F:D.192, F:N.199, F:R.241, F:R.241, E:G.33, E:T.34, E:G.35, E:K.36, E:K.36, E:K.36, E:T.37, E:W.38, E:E.172 Water bridges: F:R.240, F:R.240, E:T.37, E:D.171 Salt bridges: F:K.193, F:R.240, F:R.240, E:K.36 pi-Stacking: E:W.38, E:W.38, E:W.38 pi-Cation interactions: E:W.38 GSP.11: 14 residues within 4Å: Chain A: D.192 Chain F: P.32, G.33, T.34, G.35, K.36, T.37, W.38, F.253, I.262, H.316, S.317, L.320 Ligands: MG.12 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.33, F:T.34, F:G.35, F:K.36, F:K.36, F:T.37, F:W.38, F:S.317 Salt bridges: F:K.36 pi-Stacking: F:W.38, F:W.38, F:W.38 pi-Cation interactions: F:W.38

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.37, D.171, E.172 Chain B: R.240 Ligands: GSP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.37, A:D.171, A:D.171 MG.4: 4 residues within 4Å: Chain B: T.37, D.171, T.223 Ligands: GSP.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:T.37, B:D.171, H2O.1, H2O.1 MG.6: 4 residues within 4Å: Chain C: T.37, D.171 Chain D: R.241 Ligands: GSP.5 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:T.37, C:D.171, H2O.1, H2O.1 MG.8: 5 residues within 4Å: Chain D: T.37, D.171, E.172 Chain E: R.241 Ligands: GSP.7 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:T.37, D:D.171, H2O.1, H2O.1 MG.10: 5 residues within 4Å: Chain E: T.37, D.171, E.172 Chain F: R.241 Ligands: GSP.9 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:T.37, E:D.171, H2O.1, H2O.1 MG.12: 3 residues within 4Å: Chain F: T.37, D.171 Ligands: GSP.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.37, F:D.171

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

GTPase subunit of restriction endonuclease

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