SMTL ID : 8rif.1

Cryo-EM structure of the MCM double hexamer loaded onto dsDNA.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-mer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: I.505, Y.506, D.544, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695 Chain E: R.798, E.801 Ligands: MG.2 14 PLIP interactions: 11 interactions with chain A, 3 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:N.651, A:N.651 Salt bridges: A:K.549, A:K.549, E:R.798, E:R.798, E:R.798 ATP.14: 15 residues within 4Å: Chain I: I.505, Y.506, D.544, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695 Chain M: R.798, E.801 Ligands: MG.15 14 PLIP interactions: 11 interactions with chain I, 3 interactions with chain M Hydrogen bonds: I:Y.506, I:Y.506, I:G.546, I:T.547, I:A.548, I:K.549, I:S.550, I:N.651, I:N.651 Salt bridges: I:K.549, I:K.549, M:R.798, M:R.798, M:R.798

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.550 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.5: 3 residues within 4Å: Chain B: S.451 Chain D: R.549 Ligands: ADP.4 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: S.423 Ligands: ADP.7 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: R.577 Chain F: S.467 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467 MG.15: 2 residues within 4Å: Chain I: S.550 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.550 MG.18: 3 residues within 4Å: Chain J: S.451 Chain L: R.549 Ligands: ADP.17 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain L: S.423 Ligands: ADP.20 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain N: S.467 Ligands: ADP.24 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:S.467

10 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.341, C.344, C.364, C.367 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.341, A:C.344, A:C.364, A:C.367 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.9: 4 residues within 4Å: Chain D: C.183, 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.10: 4 residues within 4Å: Chain E: C.311, C.314, C.333, C.338 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.13: 4 residues within 4Å: Chain F: C.262, C.265, C.284, C.289 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.284, F:C.289 ZN.16: 4 residues within 4Å: Chain I: C.341, C.344, C.364, C.367 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.341, I:C.344, I:C.364, I:C.367 ZN.19: 4 residues within 4Å: Chain K: C.349, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.349, K:C.352, K:C.371, K:C.376 ZN.22: 4 residues within 4Å: Chain L: C.183, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.183, L:C.186, L:C.211, L:C.236 ZN.23: 4 residues within 4Å: Chain M: C.311, C.314, C.333, C.338 4 PLIP interactions: 4 interactions with chain M Metal complexes: M:C.311, M:C.314, M:C.333, M:C.338 ZN.26: 4 residues within 4Å: Chain N: C.262, C.265, C.284, C.289 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.262, N:C.265, N:C.284, N:C.289

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

ADP.4: 17 residues within 4Å: Chain B: S.405, I.406, Y.407, D.445, P.446, S.447, T.448, A.449, K.450, S.451, Q.452 Chain D: E.498, Q.499, I.650, R.651, E.654 Ligands: MG.5 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Y.407, B:Y.407, B:T.448, B:A.449, B:K.450, B:S.451, B:Q.452, B:Q.452, D:E.498 Salt bridges: B:K.450, D:R.651 ADP.7: 15 residues within 4Å: Chain A: H.531, I.533, R.676, R.808, E.811 Chain D: S.377, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424 Ligands: MG.8 13 PLIP interactions: 9 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:Q.424, A:H.531, A:R.676 Salt bridges: D:K.422, A:R.808, A:R.808 ADP.11: 20 residues within 4Å: Chain B: E.526, Q.527, R.577, A.734, 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.12 17 PLIP interactions: 12 interactions with chain F, 5 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:S.467, F:Q.468, F:Q.468, B:E.526, B:Q.527, B:R.577 Salt bridges: F:K.466, B:R.735, B:R.735 ADP.17: 17 residues within 4Å: Chain J: S.405, I.406, Y.407, D.445, P.446, S.447, T.448, A.449, K.450, S.451, Q.452 Chain L: E.498, Q.499, I.650, R.651, E.654 Ligands: MG.18 11 PLIP interactions: 9 interactions with chain J, 2 interactions with chain L Hydrogen bonds: J:Y.407, J:Y.407, J:T.448, J:A.449, J:K.450, J:S.451, J:Q.452, J:Q.452, L:E.498 Salt bridges: J:K.450, L:R.651 ADP.20: 15 residues within 4Å: Chain I: H.531, I.533, R.676, R.808, E.811 Chain L: S.377, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424 Ligands: MG.21 13 PLIP interactions: 9 interactions with chain L, 4 interactions with chain I Hydrogen bonds: L:F.379, L:F.379, L:G.419, L:T.420, L:A.421, L:K.422, L:S.423, L:Q.424, I:H.531, I:R.676 Salt bridges: L:K.422, I:R.808, I:R.808 ADP.24: 20 residues within 4Å: Chain J: E.526, Q.527, R.577, A.734, R.735, E.738 Chain N: 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.25 17 PLIP interactions: 5 interactions with chain J, 12 interactions with chain N Hydrogen bonds: J:E.526, J:Q.527, J:R.577, N:Y.423, N:Y.423, N:G.463, N:V.464, N:A.465, N:K.466, N:S.467, N:S.467, N:S.467, N:Q.468, N:Q.468 Salt bridges: J:R.735, J:R.735, N:K.466

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lim, C.T. et al., Cell cycle regulation has shaped replication origins in budding yeast. Nat.Struct.Mol.Biol. (2025)

Release Date

2025-01-01

Peptides

DNA replication licensing factor MCM2: AI
DNA replication licensing factor MCM3: BJ
DNA replication licensing factor MCM4: CK
Minichromosome maintenance protein 5: DL
DNA replication licensing factor MCM6: EM
DNA replication licensing factor MCM7: FN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

I
A

B
3

J
B

C
4

K
C

D
5

L
D

E
6

M
E

F
7

N
F

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

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