SMTL ID : 6ut6.1

Cryo-EM structure of the Escherichia coli McrBC complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

GDP.1: 11 residues within 4Å: Chain A: D.176, L.177, F.178, G.204, V.205, G.206, K.207, T.208, F.209, S.408, C.411 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:D.176, A:D.176, A:F.178, A:G.204, A:V.205, A:G.206, A:K.207, A:T.208, A:T.208, A:F.209 Salt bridges: A:K.207 pi-Stacking: A:F.178, A:F.209, A:F.209 pi-Cation interactions: A:F.178, A:F.367

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

GSP.2: 20 residues within 4Å: Chain B: D.176, L.177, F.178, P.203, G.204, V.205, G.206, K.207, T.208, F.209, N.333, H.407, S.408 Chain C: E.298, D.300, K.301, A.345, R.348, R.349 Ligands: MG.3 22 PLIP interactions: 15 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:D.176, B:D.176, B:F.178, B:G.204, B:V.205, B:G.206, B:K.207, B:T.208, B:F.209, C:D.300, C:R.348, C:R.349, C:R.349 Salt bridges: B:D.176, B:K.207, C:K.301, C:R.348, C:R.348 pi-Stacking: B:F.178, B:F.209, B:F.209 pi-Cation interactions: B:F.178 GSP.4: 20 residues within 4Å: Chain C: D.176, L.177, F.178, P.203, G.204, V.205, G.206, K.207, T.208, F.209, N.333, H.407, S.408 Chain D: E.298, D.300, K.301, A.345, R.348, R.349 Ligands: MG.5 25 PLIP interactions: 16 interactions with chain C, 9 interactions with chain D Hydrogen bonds: C:D.176, C:D.176, C:F.178, C:G.204, C:V.205, C:G.206, C:K.207, C:K.207, C:T.208, C:T.208, C:F.209, D:D.300, D:D.300, D:R.348, D:R.349, D:R.349 Salt bridges: C:K.207, D:K.301, D:K.301, D:R.348, D:R.348 pi-Stacking: C:F.178, C:F.209 pi-Cation interactions: C:F.178, C:F.367 GSP.6: 19 residues within 4Å: Chain D: D.176, L.177, F.178, P.203, G.204, V.205, G.206, K.207, T.208, F.209, N.333, H.407, S.408 Chain E: E.298, D.300, K.301, R.348, R.349 Ligands: MG.7 25 PLIP interactions: 15 interactions with chain D, 10 interactions with chain E Hydrogen bonds: D:D.176, D:D.176, D:F.178, D:G.204, D:V.205, D:G.206, D:K.207, D:T.208, D:F.209, E:D.300, E:K.301, E:K.301, E:R.348, E:R.348, E:R.349, E:R.349 Salt bridges: D:D.176, D:K.207, E:K.301, E:R.348, E:R.348 pi-Stacking: D:F.178, D:F.209 pi-Cation interactions: D:F.178, D:F.367 GSP.8: 22 residues within 4Å: Chain E: D.176, L.177, F.178, P.203, G.204, V.205, G.206, K.207, T.208, F.209, E.280, N.333, H.407, S.408, C.411 Chain F: E.298, D.300, K.301, A.345, R.348, R.349 Ligands: MG.9 23 PLIP interactions: 15 interactions with chain E, 8 interactions with chain F Hydrogen bonds: E:D.176, E:D.176, E:F.178, E:G.204, E:V.205, E:G.206, E:K.207, E:K.207, E:K.207, E:T.208, E:F.209, E:N.333, F:E.298, F:D.300, F:R.348, F:R.349, F:R.349 Salt bridges: E:K.207, F:K.301, F:R.348, F:R.348 pi-Stacking: E:F.178 pi-Cation interactions: E:F.367 GSP.10: 15 residues within 4Å: Chain A: D.300, K.301, R.348 Chain F: D.176, L.177, F.178, P.203, G.204, G.206, K.207, T.208, F.209, D.279, H.407, S.408 16 PLIP interactions: 13 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:D.176, F:D.176, F:F.178, F:G.204, F:G.206, F:K.207, F:K.207, F:T.208, F:T.208, F:F.209, F:D.279, A:R.348 pi-Stacking: F:F.209 pi-Cation interactions: F:F.178 Salt bridges: A:K.301, A:R.348

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain B: T.208, D.279 Chain C: R.349 Ligands: GSP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.208 MG.5: 4 residues within 4Å: Chain C: T.208, D.279 Chain D: R.349 Ligands: GSP.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.208 MG.7: 3 residues within 4Å: Chain D: T.208, D.279 Ligands: GSP.6 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.208, D:D.279, D:D.279 MG.9: 4 residues within 4Å: Chain E: T.208, D.279, E.280 Ligands: GSP.8 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.208

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

5-methylcytosine-specific restriction enzyme B: ABCDEF
Protein McrC: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

5-methylcytosine-specific restriction enzyme B

Protein McrC

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