SMTL ID : 9e2x.1

Cryo-EM structure of yeast CMG helicase stalled at G4-containing DNA template, state 2

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

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

ATP.1: 25 residues within 4Å: Chain H: S.504, I.505, Y.506, G.507, H.508, D.544, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695, F.698, V.699 Chain L: L.565, E.657, Q.658, R.708, V.797, R.798, E.801 Ligands: MG.2 16 PLIP interactions: 10 interactions with chain H, 6 interactions with chain L Hydrogen bonds: H:Y.506, H:G.507, H:H.508, H:P.545, H:T.547, H:A.548, H:K.549, H:S.550, H:Q.551, L:Q.658, L:R.798 Salt bridges: H:K.549, L:R.708, L:R.708, L:R.798, L:R.798 ATP.4: 18 residues within 4Å: Chain I: I.371, Y.372, P.411, S.412, T.413, A.414, K.415, S.416, Q.417, N.517, R.557, I.561, H.564, V.565 Chain K: R.549, I.650, R.651 Ligands: MG.5 17 PLIP interactions: 13 interactions with chain I, 4 interactions with chain K Hydrogen bonds: I:Y.372, I:Y.372, I:D.410, I:S.412, I:T.413, I:A.414, I:K.415, I:S.416, I:S.416, I:Q.417, I:N.517, K:R.651 Salt bridges: I:K.415, I:K.415, K:R.549, K:R.651, K:R.651 ATP.10: 24 residues within 4Å: Chain H: I.533, E.625, P.672, R.676, V.807, R.808, E.811 Chain K: 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, H.571, V.572, I.575 Ligands: MG.11 17 PLIP interactions: 12 interactions with chain K, 5 interactions with chain H Hydrogen bonds: K:F.379, K:F.379, K:D.417, K:G.419, K:T.420, K:A.421, K:K.422, K:S.423, K:S.423, K:N.524, H:E.811 Salt bridges: K:K.422, K:K.422, H:R.676, H:R.808, H:R.808, H:R.808 ATP.14: 25 residues within 4Å: Chain I: E.491, R.542, T.698, A.699, R.700, E.703 Chain M: E.421, I.422, Y.423, G.424, N.425, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, D.524, E.525, N.568, L.612, H.615, V.616 Ligands: MG.15 12 PLIP interactions: 10 interactions with chain M, 2 interactions with chain I Hydrogen bonds: M:Y.423, M:G.424, M:G.463, M:A.465, M:K.466, M:S.467, M:S.467, M:Q.468, M:Q.468, I:R.700, I:E.703 Salt bridges: M:K.466

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain H: S.550, D.607 Chain L: Q.658, R.708 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.550 MG.5: 2 residues within 4Å: Chain I: S.416 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.416 MG.7: 5 residues within 4Å: Chain J: K.574, S.575, D.632, S.674 Ligands: ADP.6 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:S.575, J:D.632 MG.11: 4 residues within 4Å: Chain H: R.676 Chain K: S.423, D.480 Ligands: ATP.10 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain M: S.467, D.524, E.525 Ligands: ATP.14 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:S.467, M:D.524

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain H: C.341, C.344, S.346, C.364, C.367, F.373 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.341, H:C.344, H:S.346, H:C.367 ZN.8: 5 residues within 4Å: Chain J: C.349, C.352, H.354, C.371, C.376 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.349, J:C.352, J:C.371, J:C.376 ZN.12: 4 residues within 4Å: Chain K: C.183, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.183, K:C.186, K:C.211, K:C.236 ZN.13: 7 residues within 4Å: Chain L: C.311, M.313, C.314, C.333, N.335, C.338, N.340 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.311, L:C.314, L:C.333, L:C.338 ZN.16: 7 residues within 4Å: Chain M: C.262, Q.264, C.265, C.284, S.286, C.289, G.296 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.262, M:C.265, M:C.284, M:C.289

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

ADP.6: 22 residues within 4Å: Chain J: 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 Chain M: M.448, I.450, E.542, P.686, R.687, L.690 Ligands: MG.7 9 PLIP interactions: 1 interactions with chain M, 8 interactions with chain J Salt bridges: M:R.687, J:K.574 Hydrogen bonds: J:Y.531, J:Y.531, J:S.573, J:K.574, J:S.575, J:Q.576, J:Q.576 ADP.9: 20 residues within 4Å: Chain J: Y.558, E.650, R.701, T.795, R.796, E.799 Chain L: A.536, V.537, F.538, D.576, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, L.727, I.731, L.734 13 PLIP interactions: 8 interactions with chain L, 5 interactions with chain J Hydrogen bonds: L:F.538, L:S.578, L:T.579, L:S.580, L:S.580, L:S.582, L:Q.583, J:E.650, J:E.650, J:R.701, J:T.795 Salt bridges: L:K.581, J:R.796

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

2025-03-19

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: H
DNA replication licensing factor MCM3: I
DNA replication licensing factor MCM4: J
Minichromosome maintenance protein 5: K
DNA replication licensing factor MCM6: L
DNA replication licensing factor MCM7: M
Topoisomerase 1-associated factor 1: N
Chromosome segregation in meiosis protein 3: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

H
2

I
3

J
4

K
5

L
6

M
7

N
X

O
Y

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

Chromosome segregation in meiosis protein 3

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