SMTL ID : 9e2z.1

Cryo-EM structure of human CMG helicase stalled at G4-containing DNA template

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 21 residues within 4Å: Chain A: S.484, I.485, Y.486, H.488, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, L.675, F.678, V.679 Chain E: L.386, E.478, Q.479, V.618, R.619, E.622 Ligands: MG.2 19 PLIP interactions: 10 interactions with chain A, 9 interactions with chain E Hydrogen bonds: A:Y.486, A:Y.486, A:H.488, A:G.526, A:T.527, A:A.528, A:K.529, A:S.530, A:Q.531, E:E.478, E:Q.479 Salt bridges: A:K.529, E:R.619, E:R.619 Water bridges: E:R.529, E:R.529, E:R.529, E:R.619, E:R.619

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: S.530, D.587, E.588 Chain E: R.529 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.530, H2O.1, H2O.1, H2O.1, H2O.1 MG.4: 4 residues within 4Å: Chain B: S.397 Chain D: R.513, R.611 Ligands: ATP.3 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.397, H2O.1, H2O.1, H2O.1 MG.6: 3 residues within 4Å: Chain C: S.537 Chain F: R.514 Ligands: ATP.5 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:S.537, H2O.1 MG.9: 3 residues within 4Å: Chain A: R.656 Chain D: S.388 Ligands: ATP.8 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:S.388, H2O.1, H2O.1, H2O.1 MG.12: 5 residues within 4Å: Chain C: E.612, R.663 Chain E: S.403, D.460 Ligands: ATP.11 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:S.403, H2O.2, H2O.2, H2O.2 MG.15: 3 residues within 4Å: Chain B: R.523 Chain F: S.388 Ligands: ATP.14 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:S.388, H2O.2, H2O.2, H2O.2

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

ATP.3: 25 residues within 4Å: Chain B: S.351, I.352, H.353, H.355, D.391, P.392, S.393, V.394, A.395, K.396, S.397, Q.398, N.498, I.542, H.545, V.546 Chain D: R.371, E.463, Q.464, T.509, R.513, V.610, R.611, E.614 Ligands: MG.4 23 PLIP interactions: 13 interactions with chain B, 10 interactions with chain D Hydrogen bonds: B:H.353, B:H.353, B:H.355, B:S.393, B:V.394, B:A.395, B:K.396, B:S.397, B:Q.398, B:Q.398, B:N.498, D:R.371, D:Q.464 Salt bridges: B:K.396, B:K.396, D:R.513, D:R.611, D:R.611, D:R.611 Water bridges: D:R.513, D:R.513, D:R.513, D:R.513 ATP.5: 21 residues within 4Å: Chain C: S.489, I.490, Y.491, H.493, P.532, G.533, T.534, S.535, K.536, S.537, Q.538, N.638, Y.678, L.682, H.685, L.686 Chain F: R.514, A.603, R.604, L.607 Ligands: MG.6 13 PLIP interactions: 10 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:Y.491, C:Y.491, C:H.493, C:G.533, C:S.535, C:K.536, C:S.537, C:Q.538, C:Q.538, C:N.638 Salt bridges: F:R.514, F:R.604, F:R.604 ATP.8: 28 residues within 4Å: Chain A: H.511, V.513, E.605, Q.606, P.652, R.656, V.764, R.765, E.768 Chain D: S.342, I.343, F.344, G.345, P.383, G.384, T.385, A.386, K.387, S.388, Q.389, E.446, N.489, R.528, L.532, H.535, V.536, L.539 Ligands: MG.9 25 PLIP interactions: 11 interactions with chain A, 14 interactions with chain D Hydrogen bonds: A:H.511, A:E.605, A:Q.606, D:F.344, D:D.382, D:G.384, D:T.385, D:A.386, D:K.387, D:S.388, D:Q.389, D:Q.389, D:E.446, D:N.489, D:N.489 Water bridges: A:R.656, A:R.656, A:R.765, A:R.765 Salt bridges: A:R.656, A:R.765, A:R.765, A:R.765, D:K.387, D:K.387 ATP.11: 19 residues within 4Å: Chain C: R.663, P.751, R.752, E.755 Chain E: T.357, I.358, H.359, N.361, P.398, S.399, T.400, A.401, K.402, S.403, Q.404, I.548, R.551, I.552 Ligands: MG.12 22 PLIP interactions: 14 interactions with chain E, 8 interactions with chain C Hydrogen bonds: E:H.359, E:H.359, E:N.361, E:S.399, E:T.400, E:A.401, E:K.402, E:S.403, E:Q.404, E:E.461, C:E.755 Water bridges: E:E.461, E:N.504, C:S.662, C:R.663, C:R.752, C:R.752 Salt bridges: E:K.402, E:K.402, C:R.663, C:R.752, C:R.752 ATP.14: 24 residues within 4Å: Chain B: I.380, E.472, Q.473, S.519, R.523, A.660, R.661, E.664 Chain F: E.343, I.344, Y.345, P.383, G.384, V.385, A.386, K.387, S.388, Q.389, E.446, N.489, L.533, H.536, I.537 Ligands: MG.15 24 PLIP interactions: 11 interactions with chain B, 13 interactions with chain F Hydrogen bonds: B:E.664, F:Y.345, F:Y.345, F:G.384, F:V.385, F:A.386, F:K.387, F:S.388, F:Q.389, F:Q.389, F:N.489, F:N.489 Water bridges: B:Q.473, B:Q.473, B:S.519, B:R.523, B:R.523, B:R.661 Salt bridges: B:R.523, B:R.661, B:R.661, B:R.661, F:K.387, F:K.387

4 x ZN: ZINC ION(Non-covalent)

ZN.7: 7 residues within 4Å: Chain C: C.326, V.328, C.329, H.331, C.348, C.351, S.356 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.326, C:C.329, C:C.348, C:C.351 ZN.10: 5 residues within 4Å: Chain D: C.172, C.175, C.197, T.199, C.207 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.172, D:C.175, D:C.197, D:T.199, D:C.207 ZN.13: 7 residues within 4Å: Chain E: C.158, D.160, C.161, C.180, N.182, C.185, N.187 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.158, E:C.161, E:C.180, E:C.185 ZN.16: 5 residues within 4Å: Chain F: C.184, C.187, C.206, S.208, C.211 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.184, F:C.187, F:C.206, F:C.211

2 x K: POTASSIUM ION(Non-functional Binders)

K.17: 8 residues within 4Å: Chain L: G.16, G.17, G.20, G.21, G.24, G.25, G.28, G.29 No protein-ligand interaction detected (PLIP) K.18: 8 residues within 4Å: Chain L: G.15, G.16, G.19, G.20, G.23, G.24, G.27, G.28 No protein-ligand interaction detected (PLIP)

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
Isoform 2 of DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
DNA replication licensing factor MCM5: 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 homolog: K

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

DNA replication licensing factor MCM2

Isoform 2 of DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA replication licensing factor MCM5

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 homolog

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