SMTL ID : 7nz3.1

Cryo-EM structure of apposed MukBEF-MatP monomers on DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-4-mer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.40, S.41 Chain C: S.1366, T.1367 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain B: K.40, S.41 Chain D: S.1366, T.1367 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 7 residues within 4Å: Chain A: S.1366, T.1367 Chain C: K.40, S.41, D.1406, Q.1407 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.41 MG.7: 7 residues within 4Å: Chain B: S.1366, T.1367 Chain D: K.40, S.41, D.1406, Q.1407 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.41

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

ATP.2: 24 residues within 4Å: Chain A: N.16, G.35, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, G.79, K.80, Q.1407, R.1450 Chain C: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Ligands: MG.1 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:N.16, A:N.36, A:G.37, A:A.38, A:G.39, A:K.40, A:S.41, A:S.41, A:S.41, A:T.42, A:G.76, A:G.79, A:K.80, A:Q.1407, C:R.1352, C:S.1366, C:S.1366, C:T.1367, C:G.1368, C:E.1369 Salt bridges: A:K.40, A:K.40 ATP.3: 24 residues within 4Å: Chain B: N.16, G.35, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, G.79, K.80, Q.1407, R.1450 Chain D: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Ligands: MG.4 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain D Hydrogen bonds: B:N.16, B:N.36, B:G.37, B:A.38, B:G.39, B:K.40, B:S.41, B:S.41, B:S.41, B:T.42, B:G.76, B:G.79, B:K.80, B:Q.1407, D:R.1352, D:S.1366, D:S.1366, D:T.1367, D:G.1368, D:E.1369 Salt bridges: B:K.40, B:K.40 ATP.5: 22 residues within 4Å: Chain A: Q.1269, R.1352, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Chain C: N.16, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, G.79, K.80, Q.1407, R.1450 Ligands: MG.6 23 PLIP interactions: 17 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:N.36, C:G.37, C:A.38, C:G.39, C:K.40, C:S.41, C:S.41, C:T.42, C:T.42, C:G.76, C:G.79, C:K.80, C:Q.1407, C:R.1450, A:R.1352, A:S.1366, A:S.1366, A:T.1367, A:G.1368, A:E.1369 Salt bridges: C:K.40, C:K.40, C:K.80 ATP.8: 22 residues within 4Å: Chain B: Q.1269, R.1352, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Chain D: N.16, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, G.79, K.80, Q.1407, R.1450 Ligands: MG.7 23 PLIP interactions: 17 interactions with chain D, 6 interactions with chain B Hydrogen bonds: D:N.36, D:G.37, D:A.38, D:G.39, D:K.40, D:S.41, D:S.41, D:T.42, D:T.42, D:G.76, D:G.79, D:K.80, D:Q.1407, D:R.1450, B:R.1352, B:S.1366, B:S.1366, B:T.1367, B:G.1368, B:E.1369 Salt bridges: D:K.40, D:K.40, D:K.80

4 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.9: 13 residues within 4Å: Chain A: L.289, A.290, R.292, G.293 Chain C: R.839, R.842, Q.843, T.846 Chain M: D.36, S.37, L.38, V.41, D.57 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain M Salt bridges: C:R.839 Hydrogen bonds: M:L.38 PNS.10: 13 residues within 4Å: Chain B: L.289, A.290, R.292, G.293 Chain D: R.839, R.842, Q.843, T.846 Chain N: D.36, S.37, L.38, V.41, D.57 3 PLIP interactions: 2 interactions with chain N, 1 interactions with chain D Hydrogen bonds: N:D.36, N:L.38 Salt bridges: D:R.839 PNS.11: 6 residues within 4Å: Chain C: L.289, A.290, G.293 Chain O: S.37, L.38, V.41 No protein-ligand interaction detected (PLIP) PNS.12: 6 residues within 4Å: Chain D: L.289, A.290, G.293 Chain P: S.37, L.38, V.41 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burmann, F. et al., Cryo-EM structure of MukBEF reveals DNA loop entrapment at chromosomal unloading sites. Mol.Cell (2021)

Release Date

2021-07-07

Peptides

Chromosome partition protein MukB: ABCD
Chromosome partition protein MukF: EFGH
Chromosome partition protein MukE: IJKL
Acyl carrier protein: MNOP
Macrodomain Ter protein: QRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A1

B
A2

C
B1

D
B2

E
C1

F
C2

G
D1

H
D2

I
E1

J
E2

K
F1

L
F2

M
G1

N
G2

O
H1

P
H2

Q
I1

R
I2

S
J1

T
J2

Chromosome partition protein MukB

Chromosome partition protein MukF

Chromosome partition protein MukE

Acyl carrier protein

Macrodomain Ter protein

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