SMTL ID : 8p5e.1

S. cerevisiae nexus-sCMGE after DNA replication initiation

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 DT- DT- DT- DT- DT- DT- DT: DNA (7-MER)(Non-covalent)

DT-DT-DT-DT-DT-DT-DT.1: 12 residues within 4Å: Chain A: N.613, D.614, Q.615 Chain E: I.646 Chain G: A.12, A.13, A.14, A.15, A.16, A.17, A.18, A.19 Protein-ligand interaction information (PLIP) not available

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

ATP.2: 16 residues within 4Å: Chain A: Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, V.699 Chain E: E.654, E.657, R.708, R.798, E.801 17 PLIP interactions: 13 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:A.548, A:K.549, A:S.550, A:S.550, A:Q.551, A:Q.551, E:E.654, E:E.654, E:E.657 Salt bridges: A:K.549, A:K.549, E:R.708 ATP.5: 17 residues within 4Å: Chain B: S.405, I.406, Y.407, S.447, T.448, A.449, K.450, S.451, Q.452, N.552, I.596 Chain D: E.498, Q.499, R.549, I.650, R.651 Ligands: MG.4 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:Y.407, B:Y.407, B:S.447, B:T.448, B:A.449, B:K.450, B:S.451, B:S.451, B:Q.452 Salt bridges: B:K.450, B:K.450, D:R.549, D:R.651, D:R.651, D:R.651 ATP.10: 17 residues within 4Å: Chain A: H.531, I.533, E.625, Q.626, R.676, R.808, E.811 Chain D: F.379, G.419, T.420, A.421, K.422, S.423, Q.424, N.524, V.572 Ligands: MG.8 17 PLIP interactions: 13 interactions with chain D, 4 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:S.423, D:Q.424, D:N.524, D:N.524, A:H.531, A:Q.626 Salt bridges: D:K.422, D:K.422, A:R.676, A:R.808 ATP.13: 17 residues within 4Å: Chain B: R.577, R.735, E.738 Chain F: E.421, I.422, Y.423, D.461, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, L.612, V.616 Ligands: MG.14 14 PLIP interactions: 10 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:Y.423, F:Y.423, F:D.461, F:G.463, F:V.464, F:A.465, F:K.466, F:S.467, F:S.467, F:Q.468, B:E.526, B:R.577 Salt bridges: B:R.577, B:R.735

7 x ZN: ZINC ION(Non-covalent)

ZN.3: 3 residues within 4Å: Chain A: C.344, S.346, C.367 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.344, A:C.367 ZN.7: 5 residues within 4Å: Chain C: C.349, C.352, C.371, R.373, 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.9: 3 residues within 4Å: Chain D: C.186, C.211, L.212 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.186, D:C.211 ZN.12: 4 residues within 4Å: Chain E: C.311, M.313, C.314, C.338 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.311, E:C.311, E:C.338 ZN.15: 6 residues within 4Å: Chain F: C.262, C.265, C.289, T.294, K.295, G.296 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:C.262, F:C.262, F:C.265, F:K.295, F:G.296 ZN.16: 4 residues within 4Å: Chain L: C.2108, C.2111, C.2130, C.2133 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.2108, L:C.2130, L:C.2133 ZN.17: 5 residues within 4Å: Chain L: C.2164, C.2167, C.2179, C.2181, A.2182 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:C.2164, L:C.2167, L:C.2179

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain B: S.451 Chain D: E.498, R.651 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain A: Q.626 Chain D: S.423 Ligands: ATP.10 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain F: S.467, D.524 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

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

ADP.6: 11 residues within 4Å: Chain C: P.570, S.571, T.572, S.573, K.574, S.575, N.676, L.724 Chain F: E.542, P.686, R.687 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain F Hydrogen bonds: C:T.572, C:S.573, C:K.574, C:S.575, C:S.575, C:N.676 Salt bridges: C:K.574, C:K.574, F:R.687 ADP.11: 15 residues within 4Å: Chain C: R.701, T.795, R.796 Chain E: A.536, V.537, F.538, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, L.727, H.730 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:F.538, E:S.578, E:T.579, E:S.580, E:K.581, E:S.582, E:S.582, E:H.730 Salt bridges: E:K.581, C:R.701, C:R.796

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henrikus, S.S. et al., Unwinding of a eukaryotic origin of replication visualized by cryo-EM. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-05-29

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 PSF3: H
DNA replication complex GINS protein SLD5: I
Cell division control protein 45: J
DNA polymerase epsilon subunit B: K
DNA polymerase epsilon catalytic subunit A: L
DNA replication complex GINS protein PSF1: M
DNA replication complex GINS protein PSF2: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

H
C

I
D

J
E

K
F

L
G

M
H

N
I

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 PSF3

DNA replication complex GINS protein SLD5

Cell division control protein 45

DNA polymerase epsilon subunit B

DNA polymerase epsilon catalytic subunit A

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

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