SMTL ID : 9e2y.1

Cryo-EM structure of yeast CMG helicase stalled at G4-containing DNA template, state 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

1 x DA- DG- DC- DA- DG- DA- DT: Lagging strand DNA template(Non-covalent)

DA-DG-DC-DA-DG-DA-DT.1: 16 residues within 4Å: Chain F: A.1, T.2, C.3, T.4, G.5, C.6, T.7, T.8 Chain G: K.370 Chain I: R.449, Q.450, R.451, V.452 Chain K: G.444, V.445 Chain L: T.279 7 PLIP interactions: 4 interactions with chain L, 2 interactions with chain K, 1 interactions with chain I Hydrophobic interactions: L:F.363, L:F.363 Salt bridges: L:K.364, K:K.416, K:K.416 pi-Stacking: L:F.363 Hydrogen bonds: I:R.449

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

ADP.2: 23 residues within 4Å: Chain G: S.504, I.505, Y.506, G.507, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, L.695, F.698, V.699 Chain K: L.565, E.657, Q.658, R.708, V.797, R.798, E.801 Ligands: MG.3 12 PLIP interactions: 8 interactions with chain G, 4 interactions with chain K Hydrogen bonds: G:Y.506, G:H.508, G:T.547, G:A.548, G:K.549, G:S.550, G:Q.551, K:Q.658, K:R.708 Salt bridges: G:K.549, K:R.798, K:R.798

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain G: S.550, D.607, E.608 Chain K: Q.658, R.708 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.550 MG.5: 4 residues within 4Å: Chain H: S.416, D.473 Chain J: R.549 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.416 MG.7: 4 residues within 4Å: Chain I: K.574, S.575 Chain L: R.593 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.575 MG.11: 5 residues within 4Å: Chain G: R.676 Chain J: S.423, D.480, E.481 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.423 MG.14: 4 residues within 4Å: Chain I: R.701 Chain K: K.581, S.582 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.582 MG.17: 3 residues within 4Å: Chain L: K.466, S.467 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.467

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain G: C.341, C.344, S.346, C.364, N.366, C.367 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:C.341, G:C.364 ZN.8: 5 residues within 4Å: Chain I: C.349, V.351, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.349, I:C.352, I:C.371, I:C.376 ZN.12: 5 residues within 4Å: Chain J: C.183, N.185, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.183, J:C.186, J:C.211, J:C.236 ZN.15: 8 residues within 4Å: Chain K: C.311, M.313, C.314, A.316, C.333, N.335, C.338, N.340 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.311, K:C.314, K:C.333, K:C.338 ZN.18: 5 residues within 4Å: Chain L: C.262, C.265, C.284, S.286, C.289 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.262, L:C.284, L:C.289

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

ATP.6: 21 residues within 4Å: Chain I: I.530, Y.531, D.569, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, N.676, L.720, L.724 Chain L: I.450, E.542, A.589, R.593, P.686, R.687, L.690 Ligands: MG.7 11 PLIP interactions: 7 interactions with chain I, 4 interactions with chain L Hydrogen bonds: I:Y.531, I:Y.531, I:K.574, I:S.575, I:Q.576, L:E.542 Salt bridges: I:K.574, I:K.574, L:R.593, L:R.687, L:R.687 ATP.9: 23 residues within 4Å: Chain H: S.370, I.371, Y.372, H.374, P.411, S.412, T.413, A.414, K.415, S.416, Q.417, N.517, H.564, V.565 Chain J: L.406, E.498, Q.499, T.545, R.549, I.650, R.651, E.654 Ligands: MG.5 18 PLIP interactions: 13 interactions with chain H, 5 interactions with chain J Hydrogen bonds: H:Y.372, H:Y.372, H:S.412, H:T.413, H:A.414, H:K.415, H:S.416, H:S.416, H:Q.417, H:Q.417, H:N.517, J:Q.499 Salt bridges: H:K.415, H:K.415, J:R.549, J:R.651, J:R.651, J:R.651 ATP.10: 27 residues within 4Å: Chain G: H.531, I.533, R.534, E.625, Q.626, P.672, S.675, R.676, V.807, R.808, E.811, R.815 Chain J: S.377, I.378, F.379, D.417, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, N.524, I.568, V.572 Ligands: MG.11 17 PLIP interactions: 12 interactions with chain J, 5 interactions with chain G Hydrogen bonds: J:F.379, J:F.379, J:D.417, J:G.419, J:T.420, J:A.421, J:K.422, J:S.423, J:Q.424, J:N.524, G:E.811 Salt bridges: J:K.422, J:K.422, G:R.676, G:R.808, G:R.808, G:R.808 ATP.13: 20 residues within 4Å: Chain I: R.701, T.795, R.796, E.799 Chain K: A.536, V.537, F.538, H.540, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, N.683, L.727, H.730, I.731 Ligands: MG.14 16 PLIP interactions: 3 interactions with chain I, 13 interactions with chain K Hydrogen bonds: I:R.701, I:T.795, K:F.538, K:F.538, K:S.578, K:T.579, K:S.580, K:S.580, K:K.581, K:S.582, K:S.582, K:Q.583, K:N.683 Salt bridges: I:R.796, K:K.581, K:K.581 ATP.16: 19 residues within 4Å: Chain H: R.542, A.699, R.700 Chain L: E.421, I.422, Y.423, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, E.525, N.568, L.612, H.615, V.616 Ligands: MG.17 20 PLIP interactions: 16 interactions with chain L, 4 interactions with chain H Hydrogen bonds: L:Y.423, L:Y.423, L:G.463, L:V.464, L:A.465, L:K.466, L:S.467, L:S.467, L:S.467, L:Q.468, L:Q.468, L:E.525, L:E.525, L:N.568 Salt bridges: L:K.466, L:K.466, H:R.542, H:R.700, H:R.700, H:R.700

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Batra, S. et al., G-quadruplex-stalled eukaryotic replisome structure reveals helical inchworm DNA translocation. Science (2025)

Release Date

2025-03-26

Peptides

DNA replication complex GINS protein PSF1: A
DNA replication complex GINS protein PSF2: B
DNA replication complex GINS protein PSF3: C
DNA replication complex GINS protein SLD5: D
Cell division control protein 45: E
DNA replication licensing factor MCM2: G
DNA replication licensing factor MCM3: H
DNA replication licensing factor MCM4: I
Minichromosome maintenance protein 5: J
DNA replication licensing factor MCM6: K
DNA replication licensing factor MCM7: L
Topoisomerase 1-associated factor 1: M

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

G
2

H
3

I
4

J
5

K
6

L
7

M
X

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

Cell division control protein 45

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

Minichromosome maintenance protein 5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

Topoisomerase 1-associated factor 1

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