SMTL ID : 7z13.1

S. cerevisiae CMGE dimer nucleating origin DNA melting

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: Y.506, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, D.607, V.699 Chain E: E.657, Q.658, R.708, R.798, E.801 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:Y.506, A:Y.506, A:G.546, A:T.547, A:A.548, A:K.549, A:S.550, A:S.550, A:Q.551, A:Q.551, A:D.607, E:E.657, E:Q.658, E:R.798 Salt bridges: A:K.549, A:K.549, E:R.708 ATP.3: 18 residues within 4Å: Chain B: S.405, Y.407, P.446, S.447, T.448, A.449, K.450, S.451, Q.452, N.552, I.596 Chain D: M.404, E.498, Q.499, R.549, R.651, E.654 Ligands: MG.4 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:Y.407, B:Y.407, B:S.447, B:T.448, B:A.449, B:K.450, B:S.451, B:Q.452, B:N.552, B:N.552, D:E.498 Salt bridges: B:K.450, B:K.450, D:R.549, D:R.651, D:R.651, D:R.651 ATP.7: 19 residues within 4Å: Chain A: H.531, E.625, Q.626, R.676, V.807, R.808, E.811 Chain D: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, N.524 Ligands: MG.8 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:G.419, D:T.420, D:T.420, D:A.421, D:K.422, D:S.423, D:Q.424, D:Q.424, D:N.524, D:N.524, A:Q.626 Salt bridges: D:K.422, D:K.422, A:R.676, A:R.808, A:R.808, A:R.808 ATP.12: 13 residues within 4Å: Chain B: R.577, R.735, E.738 Chain F: I.422, Y.423, P.462, G.463, V.464, A.465, K.466, S.467, L.612 Ligands: MG.13 13 PLIP interactions: 7 interactions with chain F, 6 interactions with chain B Hydrogen bonds: F:Y.423, F:Y.423, F:G.463, F:V.464, F:A.465, F:K.466, F:S.467, B:S.576, B:S.576, B:E.738 Salt bridges: B:R.577, B:R.735, B:R.735 ATP.19: 15 residues within 4Å: Chain 0: E.657, Q.658, R.708, R.798, E.801 Chain W: Y.506, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, D.607, V.699 17 PLIP interactions: 13 interactions with chain W, 4 interactions with chain 0 Hydrogen bonds: W:Y.506, W:Y.506, W:G.546, W:T.547, W:A.548, W:K.549, W:S.550, W:S.550, W:Q.551, W:Q.551, W:D.607, 0:E.657, 0:Q.658, 0:R.798 Salt bridges: W:K.549, W:K.549, 0:R.708 ATP.21: 18 residues within 4Å: Chain X: S.405, Y.407, P.446, S.447, T.448, A.449, K.450, S.451, Q.452, N.552, I.596 Chain Z: M.404, E.498, Q.499, R.549, R.651, E.654 Ligands: MG.22 17 PLIP interactions: 12 interactions with chain X, 5 interactions with chain Z Hydrogen bonds: X:Y.407, X:Y.407, X:S.447, X:T.448, X:A.449, X:K.450, X:S.451, X:Q.452, X:N.552, X:N.552, Z:E.498 Salt bridges: X:K.450, X:K.450, Z:R.549, Z:R.651, Z:R.651, Z:R.651 ATP.25: 19 residues within 4Å: Chain W: H.531, E.625, Q.626, R.676, V.807, R.808, E.811 Chain Z: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, N.524 Ligands: MG.26 19 PLIP interactions: 14 interactions with chain Z, 5 interactions with chain W Hydrogen bonds: Z:F.379, Z:F.379, Z:G.419, Z:T.420, Z:T.420, Z:A.421, Z:K.422, Z:S.423, Z:Q.424, Z:Q.424, Z:N.524, Z:N.524, W:Q.626 Salt bridges: Z:K.422, Z:K.422, W:R.676, W:R.808, W:R.808, W:R.808 ATP.30: 13 residues within 4Å: Chain 1: I.422, Y.423, P.462, G.463, V.464, A.465, K.466, S.467, L.612 Chain X: R.577, R.735, E.738 Ligands: MG.31 13 PLIP interactions: 6 interactions with chain X, 7 interactions with chain 1 Hydrogen bonds: X:S.576, X:S.576, X:E.738, 1:Y.423, 1:Y.423, 1:G.463, 1:V.464, 1:A.465, 1:K.466, 1:S.467 Salt bridges: X:R.577, X:R.735, X:R.735

14 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.341, C.344, C.364, C.367 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364, A:C.367 ZN.6: 4 residues within 4Å: Chain C: C.349, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.349, C:C.352, C:C.371, C:C.376 ZN.9: 4 residues within 4Å: Chain D: C.183, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.183, D:C.186, D:C.211, D:C.236 ZN.11: 4 residues within 4Å: Chain E: C.311, C.314, C.333, C.338 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.14: 5 residues within 4Å: Chain F: C.262, C.265, C.284, C.289, K.295 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.284, F:C.289 ZN.15: 4 residues within 4Å: Chain S: C.2108, C.2111, C.2130, C.2133 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.2108, S:C.2111, S:C.2130, S:C.2133 ZN.16: 4 residues within 4Å: Chain S: C.2164, C.2167, C.2179, C.2181 4 PLIP interactions: 4 interactions with chain S Metal complexes: S:C.2164, S:C.2167, S:C.2179, S:C.2181 ZN.17: 4 residues within 4Å: Chain V: C.2108, C.2111, C.2130, C.2133 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.2108, V:C.2111, V:C.2130, V:C.2133 ZN.18: 4 residues within 4Å: Chain V: C.2164, C.2167, C.2179, C.2181 4 PLIP interactions: 4 interactions with chain V Metal complexes: V:C.2164, V:C.2167, V:C.2179, V:C.2181 ZN.20: 4 residues within 4Å: Chain W: C.341, C.344, C.364, C.367 4 PLIP interactions: 4 interactions with chain W Metal complexes: W:C.341, W:C.344, W:C.364, W:C.367 ZN.24: 4 residues within 4Å: Chain Y: C.349, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain Y Metal complexes: Y:C.349, Y:C.352, Y:C.371, Y:C.376 ZN.27: 4 residues within 4Å: Chain Z: C.183, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain Z Metal complexes: Z:C.183, Z:C.186, Z:C.211, Z:C.236 ZN.29: 4 residues within 4Å: Chain 0: C.311, C.314, C.333, C.338 4 PLIP interactions: 4 interactions with chain 0 Metal complexes: 0:C.311, 0:C.314, 0:C.333, 0:C.338 ZN.32: 5 residues within 4Å: Chain 1: C.262, C.265, C.284, C.289, K.295 4 PLIP interactions: 4 interactions with chain 1 Metal complexes: 1:C.262, 1:C.265, 1:C.284, 1:C.289

6 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: S.451, D.508 Chain D: R.549 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.451 MG.8: 2 residues within 4Å: Chain D: S.423 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.423 MG.13: 2 residues within 4Å: Chain F: S.467 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.22: 4 residues within 4Å: Chain X: S.451, D.508 Chain Z: R.549 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain X Metal complexes: X:S.451 MG.26: 2 residues within 4Å: Chain Z: S.423 Ligands: ATP.25 1 PLIP interactions: 1 interactions with chain Z Metal complexes: Z:S.423 MG.31: 2 residues within 4Å: Chain 1: S.467 Ligands: ATP.30 No protein-ligand interaction detected (PLIP)

4 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.5: 12 residues within 4Å: Chain C: P.570, T.572, S.573, K.574, S.575, Q.576, L.720, L.724 Chain F: R.593, P.686, R.687, L.690 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:P.570, C:S.573, C:K.574, C:S.575, C:S.575, C:S.575, C:Q.576 Salt bridges: F:R.593, F:R.687, F:R.687 ADP.10: 13 residues within 4Å: Chain C: T.795, R.796, E.799 Chain E: V.537, F.538, S.578, T.579, S.580, K.581, S.582, L.727, H.730, I.731 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain C Hydrogen bonds: E:F.538, E:F.538, E:S.578, E:T.579, E:S.580, E:K.581, E:S.582, E:S.582, E:H.730, C:R.796, C:E.799 Salt bridges: C:R.796 ADP.23: 12 residues within 4Å: Chain 1: R.593, P.686, R.687, L.690 Chain Y: P.570, T.572, S.573, K.574, S.575, Q.576, L.720, L.724 10 PLIP interactions: 7 interactions with chain Y, 3 interactions with chain 1 Hydrogen bonds: Y:P.570, Y:S.573, Y:K.574, Y:S.575, Y:S.575, Y:S.575, Y:Q.576 Salt bridges: 1:R.593, 1:R.687, 1:R.687 ADP.28: 13 residues within 4Å: Chain 0: V.537, F.538, S.578, T.579, S.580, K.581, S.582, L.727, H.730, I.731 Chain Y: T.795, R.796, E.799 12 PLIP interactions: 9 interactions with chain 0, 3 interactions with chain Y Hydrogen bonds: 0:F.538, 0:F.538, 0:S.578, 0:T.579, 0:S.580, 0:K.581, 0:S.582, 0:S.582, 0:H.730, Y:R.796, Y:E.799 Salt bridges: Y:R.796

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lewis, J.S. et al., Mechanism of replication origin melting nucleated by CMG helicase assembly. Nature (2022)

Release Date

2022-06-15

Peptides

DNA replication licensing factor MCM2: AW
DNA replication licensing factor MCM3: BX
DNA replication licensing factor MCM4: CY
DNA helicase: DZ
DNA replication licensing factor MCM6: E0
DNA replication licensing factor MCM7: F1
DNA replication complex GINS protein PSF3: IO
DNA replication complex GINS protein SLD5: JP
Cell division control protein 45: KQ
DNA polymerase epsilon subunit B: LR
DNA replication complex GINS protein PSF1: MT
DNA replication complex GINS protein PSF2: NU
DNA polymerase epsilon catalytic subunit A: SV

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

W
a

B
3

X
b

C
4

Y
c

D
5

Z
d

E
6

0
e

F
7

1
f

I
C

O
J

J
D

P
K

K
E

Q
L

L
F

R
M

M
H

T
O

N
I

U
P

S
N

V
Q

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA helicase

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

Cell division control protein 45

DNA polymerase epsilon subunit B

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

DNA polymerase epsilon catalytic subunit A

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