SMTL ID : 7nz2.1

Cryo-EM structure of the MukBEF-MatP-DNA tetrad

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-8-4-8-8-8-mer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: K.40, S.41 Chain E: 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 F: S.1366, T.1367 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain C: K.40, S.41 Chain G: S.1366, T.1367 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain D: K.40, S.41 Chain H: S.1366, T.1367 Ligands: ATP.8 No protein-ligand interaction detected (PLIP) MG.9: 7 residues within 4Å: Chain A: S.1366, T.1367 Chain E: K.40, S.41, D.1406, Q.1407 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.41 MG.11: 7 residues within 4Å: Chain B: S.1366, T.1367 Chain F: K.40, S.41, D.1406, Q.1407 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.41 MG.14: 7 residues within 4Å: Chain C: S.1366, T.1367 Chain G: K.40, S.41, D.1406, Q.1407 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.41 MG.16: 7 residues within 4Å: Chain D: S.1366, T.1367 Chain H: K.40, S.41, D.1406, Q.1407 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.41

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

ATP.2: 26 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, H.78, G.79, K.80, Q.1407, P.1435, R.1450 Chain E: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Ligands: MG.1 23 PLIP interactions: 15 interactions with chain A, 8 interactions with chain E Hydrogen bonds: A:N.16, A:N.36, A:G.37, A:G.39, A:K.40, A:S.41, A:S.41, A:S.41, A:T.42, A:T.42, A:G.76, A:K.80, A:Q.1407, E:R.1352, E:S.1366, E:S.1366, E:T.1367, E:T.1367, E:G.1368, E:E.1369, E:E.1369 Salt bridges: A:K.40, A:K.40 ATP.3: 26 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, H.78, G.79, K.80, Q.1407, P.1435, R.1450 Chain F: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Ligands: MG.4 23 PLIP interactions: 15 interactions with chain B, 8 interactions with chain F Hydrogen bonds: B:N.16, B:N.36, B:G.37, B:G.39, B:K.40, B:S.41, B:S.41, B:S.41, B:T.42, B:T.42, B:G.76, B:K.80, B:Q.1407, F:R.1352, F:S.1366, F:S.1366, F:T.1367, F:T.1367, F:G.1368, F:E.1369, F:E.1369 Salt bridges: B:K.40, B:K.40 ATP.5: 26 residues within 4Å: Chain C: N.16, G.35, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, H.78, G.79, K.80, Q.1407, P.1435, R.1450 Chain G: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Ligands: MG.6 23 PLIP interactions: 15 interactions with chain C, 8 interactions with chain G Hydrogen bonds: C:N.16, C:N.36, C:G.37, C:G.39, C:K.40, C:S.41, C:S.41, C:S.41, C:T.42, C:T.42, C:G.76, C:K.80, C:Q.1407, G:R.1352, G:S.1366, G:S.1366, G:T.1367, G:T.1367, G:G.1368, G:E.1369, G:E.1369 Salt bridges: C:K.40, C:K.40 ATP.8: 26 residues within 4Å: Chain D: N.16, G.35, N.36, G.37, A.38, G.39, K.40, S.41, T.42, G.76, H.78, G.79, K.80, Q.1407, P.1435, R.1450 Chain H: Q.1269, R.1352, G.1363, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Ligands: MG.7 23 PLIP interactions: 8 interactions with chain H, 15 interactions with chain D Hydrogen bonds: H:R.1352, H:S.1366, H:S.1366, H:T.1367, H:T.1367, H:G.1368, H:E.1369, H:E.1369, D:N.16, D:N.36, D:G.37, D:G.39, D:K.40, D:S.41, D:S.41, D:S.41, D:T.42, D:T.42, D:G.76, D:K.80, D:Q.1407 Salt bridges: D:K.40, D:K.40 ATP.10: 22 residues within 4Å: Chain A: Q.1269, R.1352, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Chain E: 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.9 21 PLIP interactions: 14 interactions with chain E, 7 interactions with chain A Hydrogen bonds: E:N.36, E:G.37, E:A.38, E:G.39, E:K.40, E:S.41, E:T.42, E:T.42, E:G.76, E:K.80, E:Q.1407, A:R.1352, A:S.1366, A:S.1366, A:T.1367, A:G.1368, A:E.1369, A:E.1369 Salt bridges: E:K.40, E:K.40, E:K.80 ATP.12: 22 residues within 4Å: Chain B: Q.1269, R.1352, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Chain F: 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.11 22 PLIP interactions: 15 interactions with chain F, 7 interactions with chain B Hydrogen bonds: F:N.36, F:G.37, F:A.38, F:G.39, F:K.40, F:S.41, F:S.41, F:T.42, F:T.42, F:G.76, F:K.80, F:Q.1407, B:R.1352, B:S.1366, B:S.1366, B:T.1367, B:G.1368, B:E.1369, B:E.1369 Salt bridges: F:K.40, F:K.40, F:K.80 ATP.13: 22 residues within 4Å: Chain C: Q.1269, R.1352, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Chain G: 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.14 22 PLIP interactions: 7 interactions with chain C, 15 interactions with chain G Hydrogen bonds: C:R.1352, C:S.1366, C:S.1366, C:T.1367, C:G.1368, C:E.1369, C:E.1369, G:N.36, G:G.37, G:A.38, G:G.39, G:K.40, G:S.41, G:S.41, G:T.42, G:T.42, G:G.76, G:K.80, G:Q.1407 Salt bridges: G:K.40, G:K.40, G:K.80 ATP.15: 22 residues within 4Å: Chain D: Q.1269, R.1352, A.1364, L.1365, S.1366, T.1367, G.1368, E.1369 Chain H: 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.16 23 PLIP interactions: 15 interactions with chain H, 8 interactions with chain D Hydrogen bonds: H:N.36, H:G.37, H:A.38, H:G.39, H:K.40, H:S.41, H:S.41, H:T.42, H:T.42, H:G.76, H:K.80, H:Q.1407, D:R.1352, D:S.1366, D:S.1366, D:T.1367, D:T.1367, D:G.1368, D:E.1369, D:E.1369 Salt bridges: H:K.40, H:K.40, H:K.80

8 x PNS: 4'-PHOSPHOPANTETHEINE(Covalent)

PNS.17: 16 residues within 4Å: Chain A: L.285, D.286, L.289, A.290, R.292, G.293 Chain E: R.839, R.842, Q.843, T.846 Chain U: D.36, S.37, L.38, D.39, V.41, D.57 3 PLIP interactions: 2 interactions with chain U, 1 interactions with chain E Hydrogen bonds: U:D.36, U:L.38 Salt bridges: E:R.839 PNS.18: 16 residues within 4Å: Chain B: L.285, D.286, L.289, A.290, R.292, G.293 Chain F: R.839, R.842, Q.843, T.846 Chain V: D.36, S.37, L.38, D.39, V.41, D.57 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain F Hydrogen bonds: V:D.36, V:L.38 Salt bridges: F:R.839 PNS.19: 16 residues within 4Å: Chain C: L.285, D.286, L.289, A.290, R.292, G.293 Chain G: R.839, R.842, Q.843, T.846 Chain W: D.36, S.37, L.38, D.39, V.41, D.57 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain W Salt bridges: G:R.839 Hydrogen bonds: W:L.38 PNS.20: 16 residues within 4Å: Chain D: L.285, D.286, L.289, A.290, R.292, G.293 Chain H: R.839, R.842, Q.843, T.846 Chain X: D.36, S.37, L.38, D.39, V.41, D.57 3 PLIP interactions: 2 interactions with chain X, 1 interactions with chain H Hydrogen bonds: X:D.36, X:L.38 Salt bridges: H:R.839 PNS.21: 6 residues within 4Å: Chain E: L.289, A.290, G.293 Chain Y: S.37, L.38, V.41 No protein-ligand interaction detected (PLIP) PNS.22: 6 residues within 4Å: Chain F: L.289, A.290, G.293 Chain Z: S.37, L.38, V.41 No protein-ligand interaction detected (PLIP) PNS.23: 6 residues within 4Å: Chain 0: S.37, L.38, V.41 Chain G: L.289, A.290, G.293 No protein-ligand interaction detected (PLIP) PNS.24: 6 residues within 4Å: Chain 1: S.37, L.38, V.41 Chain H: L.289, A.290, G.293 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: ABCDEFGH
Chromosome partition protein MukF: IJKL
Chromosome partition protein MukE: MNOPQRST
Acyl carrier protein: UVWXYZ01
Macrodomain Ter protein: 23456789

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A1

B
A2

C
A3

D
A4

E
B1

F
B2

G
B3

H
B4

I
C1

J
C2

K
D1

L
D2

M
E1

N
E2

O
E3

P
E4

Q
F1

R
F2

S
F3

T
F4

U
G1

V
G2

W
G3

X
G4

Y
H1

Z
H2

0
H3

1
H4

2
I1

3
I2

4
I3

5
I4

6
J1

7
J2

8
J3

9
J4

Chromosome partition protein MukB

Chromosome partition protein MukF

Chromosome partition protein MukE

Acyl carrier protein

Macrodomain Ter protein

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