SMTL ID : 8btg.1

Cryo-EM structure of the bacterial replication origin opening basal unwinding system

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: D.214, D.215 Ligands: ATP.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.215, A:D.215 MG.3: 5 residues within 4Å: Chain B: K.157, D.214, D.215, S.246 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.214 MG.5: 5 residues within 4Å: Chain C: K.157, D.214, D.215, S.246 Ligands: ATP.6 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain D: K.157, D.214, D.215, S.246 Ligands: ATP.8 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.214, D:D.215 MG.9: 3 residues within 4Å: Chain D: R.264 Chain E: R.313 Ligands: ATP.10 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain E: R.264 Chain F: R.313 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain F: W.267 Chain G: R.313 Ligands: ATP.14 No protein-ligand interaction detected (PLIP)

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

ATP.2: 13 residues within 4Å: Chain A: Y.115, V.153, G.154, L.155, G.156, K.157, T.158, D.214, D.215, I.284, I.312, R.313 Ligands: MG.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.115, A:G.154, A:L.155, A:G.156, A:T.158, A:T.158, A:D.215, A:R.313 ATP.4: 18 residues within 4Å: Chain A: R.264, W.267 Chain B: K.114, Y.115, F.120, V.121, V.153, G.154, L.155, G.156, K.157, T.158, H.159, K.288, I.312, R.313, E.316 Ligands: MG.3 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.115, B:V.121, B:V.121, B:N.126, B:G.154, B:L.155, B:G.156, B:K.157, B:T.158, B:T.158, B:H.159, B:H.159, B:K.288 Salt bridges: B:K.157, B:R.313, B:R.313, B:R.313, A:R.264 pi-Stacking: B:H.159, B:H.159 ATP.6: 21 residues within 4Å: Chain B: R.264 Chain C: Y.115, T.119, F.120, V.121, N.126, G.152, V.153, G.154, L.155, G.156, K.157, T.158, H.159, D.214, I.284, K.288, I.312, R.313, E.316 Ligands: MG.5 22 PLIP interactions: 21 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:Y.115, C:V.121, C:V.121, C:N.126, C:G.152, C:G.154, C:L.155, C:G.156, C:G.156, C:K.157, C:T.158, C:T.158, C:H.159, C:H.159, C:D.214, C:K.288 Salt bridges: C:K.157, C:K.157, C:R.313, C:R.313, B:R.264 pi-Stacking: C:H.159 ATP.8: 22 residues within 4Å: Chain C: R.260, R.264, W.267 Chain D: Y.115, T.119, F.120, V.121, G.152, V.153, G.154, L.155, G.156, K.157, T.158, H.159, D.214, D.215, I.284, K.288, I.312, R.313 Ligands: MG.7 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:V.121, D:V.121, D:G.152, D:G.154, D:L.155, D:G.156, D:K.157, D:T.158, D:T.158, D:H.159, D:H.159, D:K.288, D:R.313, C:R.260, C:R.264 Salt bridges: D:K.157, D:K.157, D:R.313, D:R.313 pi-Stacking: D:H.159 ATP.10: 21 residues within 4Å: Chain D: R.264 Chain E: Y.115, F.120, V.121, N.126, G.152, V.153, G.154, L.155, G.156, K.157, T.158, H.159, D.214, D.215, I.284, K.288, I.312, R.313, E.316 Ligands: MG.9 23 PLIP interactions: 21 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:Y.115, E:V.121, E:V.121, E:N.126, E:G.154, E:L.155, E:G.156, E:G.156, E:K.157, E:T.158, E:T.158, E:H.159, E:H.159, E:D.215, E:K.288, D:W.267 Salt bridges: E:K.157, E:K.157, E:R.313, E:R.313, E:R.313, D:R.264 pi-Stacking: E:H.159 ATP.12: 19 residues within 4Å: Chain E: R.264, W.267 Chain F: Y.115, V.121, V.153, G.154, L.155, G.156, K.157, T.158, H.159, D.214, D.215, I.284, K.288, I.312, R.313, E.316 Ligands: MG.11 23 PLIP interactions: 22 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Y.115, F:Y.115, F:V.121, F:V.121, F:G.154, F:L.155, F:G.156, F:K.157, F:T.158, F:T.158, F:T.158, F:H.159, F:D.214, F:D.215, F:K.288, F:E.316 Salt bridges: F:K.157, F:K.157, F:R.313, F:R.313, F:R.313, E:R.264 pi-Stacking: F:H.159 ATP.14: 21 residues within 4Å: Chain F: W.267 Chain G: Y.115, F.120, V.121, N.126, G.152, V.153, G.154, L.155, G.156, K.157, T.158, H.159, D.214, D.215, I.284, K.288, I.312, R.313, E.316 Ligands: MG.13 21 PLIP interactions: 20 interactions with chain G, 1 interactions with chain F Hydrogen bonds: G:V.121, G:V.121, G:N.126, G:G.154, G:L.155, G:G.156, G:G.156, G:K.157, G:T.158, G:T.158, G:H.159, G:H.159, G:D.215, G:K.288, F:W.267 Salt bridges: G:K.157, G:K.157, G:R.313, G:R.313, G:R.313 pi-Stacking: G:H.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pelliciari, S. et al., The bacterial replication origin BUS promotes nucleobase capture. Nat Commun (2023)

Release Date

2024-02-14

Peptides

Chromosomal replication initiator protein DnaA: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Chromosomal replication initiator protein DnaA