SMTL ID : 8kg8.1

Yeast replisome in state II

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-3-1-1-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: C.341, C.344, G.345, C.364, N.366, C.367 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364 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.7: 5 residues within 4Å: Chain D: C.183, C.186, C.211, S.213, 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.10: 6 residues within 4Å: Chain E: C.311, M.313, C.314, A.316, C.333, C.338 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:C.311, E:M.313, E:C.314, E:C.333, E:C.338 ZN.13: 7 residues within 4Å: Chain F: C.262, Q.264, C.265, C.284, C.289, T.294, G.296 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.262, F:C.284, F:C.289 ZN.16: 4 residues within 4Å: Chain Q: C.2108, C.2111, C.2130, C.2133 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.2108, Q:C.2111, Q:C.2130, Q:C.2133 ZN.17: 4 residues within 4Å: Chain Q: C.2164, C.2167, C.2179, C.2181 4 PLIP interactions: 4 interactions with chain Q Metal complexes: Q:C.2164, Q:C.2167, Q:C.2179, Q:C.2181

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

ADP.2: 21 residues within 4Å: Chain A: S.504, I.505, Y.506, H.508, D.544, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, L.695, V.699 Chain E: E.657, Q.658, R.708, V.797, R.798, E.801 Ligands: MG.3 14 PLIP interactions: 10 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:Q.551, A:Q.551, E:R.708, E:E.801 Salt bridges: A:K.549, E:R.798, E:R.798 ADP.4: 20 residues within 4Å: Chain B: S.370, I.371, Y.372, H.374, D.410, P.411, S.412, T.413, A.414, K.415, S.416, Q.417, V.565 Chain D: E.498, Q.499, R.549, I.650, R.651, E.654 Ligands: MG.5 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain D Hydrogen bonds: B:Y.372, B:Y.372, B:D.410, B:S.412, B:T.413, B:A.414, B:K.415, B:S.416, B:Q.417, B:Q.417 Salt bridges: B:K.415, D:R.549, D:R.651, D:R.651

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: S.550 Chain E: R.708, R.798 Ligands: ADP.2 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: Q.499 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: Q.626, R.808 Chain D: S.423 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.423 MG.11: 5 residues within 4Å: Chain C: E.650, R.701 Chain E: S.582, D.639 Ligands: AGS.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.582 MG.14: 3 residues within 4Å: Chain B: R.700 Chain F: S.467 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.8: 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.9 21 PLIP interactions: 13 interactions with chain D, 8 interactions with chain A Hydrogen bonds: D:F.379, D:F.379, D:N.381, D:G.419, D:T.420, D:T.420, D:T.420, D:A.421, D:K.422, D:S.423, D:S.423, D:Q.424, A:H.531, A:Q.626, A:R.676, A:R.676, A:R.808, A:R.808 Salt bridges: D:K.422, A:R.808, A:R.808 AGS.12: 20 residues within 4Å: Chain C: E.650, R.701, 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, D.639, E.640, N.683, L.727, I.731 Ligands: MG.11 13 PLIP interactions: 10 interactions with chain E, 3 interactions with chain C Hydrogen bonds: E:F.538, E:F.538, E:K.581, E:K.581, E:S.582, E:Q.583, E:Q.583, E:E.640, E:N.683, C:R.701, C:E.799 Salt bridges: E:K.581, C:R.701 AGS.15: 19 residues within 4Å: Chain B: S.538, R.542, A.699, R.700 Chain F: E.421, I.422, Y.423, D.461, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, E.525, N.568, L.612 Ligands: MG.14 14 PLIP interactions: 11 interactions with chain F, 3 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, F:S.467, F:E.525, F:N.568, B:R.542, B:R.542 Salt bridges: F:K.466, B:R.700

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Z. et al., Synergism between CMG helicase and leading strand DNA polymerase at replication fork. Nat Commun (2023)

Release Date

2023-12-06

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
DNA polymerase alpha-binding protein: LMN
DNA polymerase epsilon catalytic subunit A: Q
DNA polymerase epsilon subunit B: R

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

L
F

M
G

N
H

Q
M

R
N

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

DNA polymerase alpha-binding protein

DNA polymerase epsilon catalytic subunit A

DNA polymerase epsilon subunit B

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