SMTL ID : 9e2w.1

Cryo-EM structure of yeast CMG helicase stalled at G4-containing DNA template, state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: 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 E: L.565, E.657, Q.658, R.708, V.797, R.798, E.801 Ligands: MG.2 12 PLIP interactions: 4 interactions with chain E, 8 interactions with chain A Hydrogen bonds: E:Q.658, E:R.708, A:Y.506, A:T.547, A:A.548, A:K.549, A:S.550, A:S.550, A:Q.551 Salt bridges: E:R.798, E:R.798, A:K.549

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.550, D.607, E.608 Chain E: R.708 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.5: 3 residues within 4Å: Chain B: S.416 Chain D: R.549 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.416 MG.7: 4 residues within 4Å: Chain C: S.575, D.632, S.674 Ligands: ATP.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:S.575, C:D.632 MG.10: 4 residues within 4Å: Chain A: R.676 Chain D: S.423, D.480 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain C: E.650 Chain E: S.582, D.639 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.582 MG.16: 4 residues within 4Å: Chain F: K.466, S.467, D.524 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 8 residues within 4Å: Chain A: C.341, C.344, S.346, L.348, C.364, N.366, C.367, F.373 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.341, A:C.364 ZN.8: 5 residues within 4Å: Chain C: C.349, C.352, H.354, 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.11: 5 residues within 4Å: Chain D: C.183, N.185, 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.14: 8 residues within 4Å: Chain E: C.311, M.313, C.314, A.316, C.333, N.335, C.338, N.340 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.17: 5 residues within 4Å: Chain F: C.262, C.265, C.284, S.286, C.289 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.262, F:C.284, F:C.289

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

ATP.4: 23 residues within 4Å: Chain B: S.370, I.371, Y.372, H.374, P.411, S.412, T.413, A.414, K.415, S.416, Q.417, N.517, I.561, H.564, V.565 Chain D: L.406, E.498, Q.499, R.549, I.650, R.651, E.654 Ligands: MG.5 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:Y.372, B:Y.372, B:S.412, B:T.413, B:A.414, B:K.415, B:S.416, B:S.416, B:S.416, B:Q.417, B:Q.417, B:N.517 Salt bridges: B:K.415, B:K.415, D:R.549, D:R.651, D:R.651, D:R.651 ATP.6: 24 residues within 4Å: Chain C: S.529, I.530, Y.531, L.533, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, N.676, L.720, H.723, L.724, L.727 Chain F: E.542, A.589, S.592, R.593, P.686, R.687, L.690 Ligands: MG.7 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:Y.531, C:Y.531, C:S.573, C:K.574, C:S.575, C:Q.576, C:Q.576, C:N.676, F:R.687 Salt bridges: C:K.574, C:K.574, F:R.593, F:R.687, F:R.687 ATP.9: 25 residues within 4Å: Chain A: H.531, I.533, E.625, Q.626, P.672, 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, I.568, H.571, V.572, I.575 Ligands: MG.10 19 PLIP interactions: 12 interactions with chain D, 7 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:G.419, D:T.420, D:A.421, D:K.422, D:S.423, D:Q.424, D:Q.424, D:N.524, A:H.531, A:Q.626, 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: 21 residues within 4Å: Chain C: E.650, R.701, T.795, R.796, E.799 Chain E: 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.13 16 PLIP interactions: 12 interactions with chain E, 4 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:Q.583, E:N.683, C:T.795, C:R.796 Salt bridges: E:K.581, E:K.581, C:R.796, C:R.796 ATP.15: 17 residues within 4Å: Chain B: R.542, A.699, R.700, E.703 Chain F: I.422, Y.423, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, N.568, L.612, V.616 Ligands: MG.16 12 PLIP interactions: 7 interactions with chain F, 5 interactions with chain B Hydrogen bonds: F:Y.423, F:G.463, F:K.466, F:S.467, F:S.467, F:Q.468, F:N.568, B:E.703 Salt bridges: B:R.542, B:R.700, B:R.700, B: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 licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
Minichromosome maintenance protein 5: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F
DNA replication complex GINS protein PSF1: G
DNA replication complex GINS protein PSF2: H
DNA replication complex GINS protein PSF3: I
DNA replication complex GINS protein SLD5: J
Cell division control protein 45: K
Topoisomerase 1-associated factor 1: N
Chromosome segregation in meiosis protein 3: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
A

H
B

I
C

J
D

K
E

N
X

O
Y

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

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

Topoisomerase 1-associated factor 1

Chromosome segregation in meiosis protein 3

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