SMTL ID : 7v3v.1

Cryo-EM structure of MCM double hexamer bound with DDK in State I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-1-1-mer

Ligands

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

AGS.1: 19 residues within 4Å: Chain A: S.504, I.505, Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, E.608, N.651, L.695 Chain E: R.708, V.797, R.798, E.801 Ligands: MG.2 17 PLIP interactions: 12 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:Y.506, A:Y.506, A:G.546, A:T.547, A:T.547, A:A.548, A:K.549, A:S.550, A:Q.551, A:Q.551, A:N.651, E:R.708, E:R.798, E:R.798 Salt bridges: A:K.549, E:R.798, E:R.798 AGS.6: 23 residues within 4Å: Chain C: S.529, I.530, Y.531, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, E.633, N.676, L.720, L.724 Chain F: M.448, I.450, E.542, A.589, R.593, P.686, R.687, L.690 Ligands: MG.7 21 PLIP interactions: 14 interactions with chain C, 7 interactions with chain F Hydrogen bonds: C:Y.531, C:Y.531, C:S.571, C:T.572, C:T.572, C:S.573, C:S.573, C:K.574, C:S.575, C:Q.576, C:Q.576, C:Q.576, C:N.676, F:E.542, F:R.593, F:R.593, F:R.687, F:R.687 Salt bridges: C:K.574, F:R.687, F:R.687 AGS.10: 19 residues within 4Å: Chain A: H.531, I.533, S.675, 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, E.481, N.524 Ligands: MG.11 11 PLIP interactions: 10 interactions with chain D, 1 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, D:N.524, A:H.531 Salt bridges: D:K.422 AGS.13: 21 residues within 4Å: Chain C: Y.558, E.650, P.697, R.701, T.795, R.796, 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, N.683, L.727 Ligands: MG.9 21 PLIP interactions: 7 interactions with chain C, 14 interactions with chain E Hydrogen bonds: C:R.701, C:R.701, C:T.795, C:R.796, C:E.799, E:F.538, E:F.538, E:S.578, E:T.579, E:T.579, E:S.580, E:S.580, E:K.581, E:K.581, E:S.582, E:Q.583, E:N.683, E:N.683 Salt bridges: C:R.796, C:R.796, E:K.581 AGS.15: 25 residues within 4Å: Chain B: L.399, E.491, Q.492, S.538, R.542, A.699, R.700, E.703 Chain F: E.421, I.422, Y.423, N.425, D.461, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, E.525, N.568, L.612, V.616 Ligands: MG.16 20 PLIP interactions: 13 interactions with chain F, 7 interactions with chain B Hydrogen bonds: F:Y.423, F:Y.423, F:N.425, F:G.463, F:V.464, F:A.465, F:K.466, F:S.467, F:S.467, F:Q.468, F:E.525, F:N.568, B:E.491, B:S.538, B:R.542, B:R.542, B:R.700 Salt bridges: F:K.466, B:R.700, B:R.700 AGS.18: 18 residues within 4Å: Chain G: S.504, I.505, Y.506, H.508, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, N.651, L.695, F.698 Chain K: V.797, R.798, E.801 Ligands: MG.19 16 PLIP interactions: 5 interactions with chain K, 11 interactions with chain G Hydrogen bonds: K:R.798, K:R.798, K:E.801, G:Y.506, G:Y.506, G:G.546, G:T.547, G:T.547, G:A.548, G:K.549, G:S.550, G:S.550, G:Q.551 Salt bridges: K:R.798, K:R.798, G:K.549 AGS.23: 22 residues within 4Å: Chain I: S.529, I.530, Y.531, D.569, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, E.633, N.676, L.720, L.724 Chain L: I.450, A.589, R.593, P.686, R.687, L.690 Ligands: MG.24 17 PLIP interactions: 11 interactions with chain I, 6 interactions with chain L Hydrogen bonds: I:Y.531, I:Y.531, I:S.571, I:T.572, I:T.572, I:S.573, I:S.573, I:K.574, I:S.575, I:Q.576, L:R.593, L:R.593, L:R.687, L:R.687 Salt bridges: I:K.574, L:R.687, L:R.687 AGS.27: 16 residues within 4Å: Chain G: H.531, V.807, R.808, E.811 Chain J: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, N.524 Ligands: MG.28 14 PLIP interactions: 11 interactions with chain J, 3 interactions with chain G Hydrogen bonds: J:F.379, J:F.379, J:G.419, J:T.420, J:A.421, J:K.422, J:K.422, J:S.423, J:Q.424, J:N.524, G:H.531 Salt bridges: J:K.422, G:R.808, G:R.808 AGS.30: 20 residues within 4Å: Chain I: E.650, P.697, R.701, T.795, R.796, E.799 Chain K: A.536, V.537, F.538, H.540, P.577, S.578, T.579, S.580, K.581, S.582, Q.583, N.683, L.727 Ligands: MG.26 20 PLIP interactions: 14 interactions with chain K, 6 interactions with chain I Hydrogen bonds: K:F.538, K:F.538, K:S.578, K:T.579, K:T.579, K:T.579, K:S.580, K:S.580, K:K.581, K:S.582, K:Q.583, K:Q.583, K:Q.583, K:N.683, I:R.701, I:R.701, I:R.796, I:E.799 Salt bridges: I:R.796, I:R.796 AGS.32: 23 residues within 4Å: Chain H: L.399, E.491, Q.492, S.538, R.542, A.699, R.700, E.703 Chain L: E.421, I.422, Y.423, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, E.525, N.568, L.612, V.616 Ligands: MG.33 18 PLIP interactions: 6 interactions with chain H, 12 interactions with chain L Hydrogen bonds: H:E.491, H:Q.492, H:R.542, H:R.542, L:Y.423, L:Y.423, L:G.463, L:V.464, L:A.465, L:K.466, L:S.467, L:Q.468, L:Q.468, L:E.525, L:N.568 Salt bridges: H:R.700, H:R.700, L:K.466 AGS.35: 20 residues within 4Å: Chain M: I.39, G.40, G.42, T.43, F.44, S.45, V.47, A.74, K.76, E.90, P.121, Y.122, Y.123, H.125, D.163, T.167, N.168, L.170, V.181, D.182 12 PLIP interactions: 12 interactions with chain M Hydrogen bonds: M:T.43, M:F.44, M:S.45, M:P.121, M:Y.123, M:D.163, M:T.167, M:D.182, M:D.182, M:D.182 Salt bridges: M:K.76, M:K.76

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: S.550, D.607 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.5: 2 residues within 4Å: Chain B: S.416 Ligands: ADP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.416 MG.7: 4 residues within 4Å: Chain C: S.575, D.632 Chain F: R.593 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.575 MG.9: 4 residues within 4Å: Chain C: E.650 Chain E: S.582, D.639 Ligands: AGS.13 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Metal complexes: C:E.650, E:S.582 MG.11: 3 residues within 4Å: Chain D: S.423, D.480 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.423 MG.16: 4 residues within 4Å: Chain F: S.467, D.524, E.525 Ligands: AGS.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467 MG.19: 2 residues within 4Å: Chain G: S.550 Ligands: AGS.18 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.550 MG.22: 2 residues within 4Å: Chain H: S.416 Ligands: ADP.21 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.416 MG.24: 5 residues within 4Å: Chain I: S.575, D.632, E.633 Chain L: R.593 Ligands: AGS.23 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:S.575 MG.26: 4 residues within 4Å: Chain I: E.650 Chain K: S.582, D.639 Ligands: AGS.30 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain I Metal complexes: K:S.582, I:E.650 MG.28: 3 residues within 4Å: Chain G: E.625 Chain J: S.423 Ligands: AGS.27 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.423 MG.33: 4 residues within 4Å: Chain L: S.467, D.524, E.525 Ligands: AGS.32 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.467

11 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.341, C.344, S.346, 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.8: 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.12: 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.14: 5 residues within 4Å: Chain E: C.311, C.314, C.333, N.335, 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.17: 5 residues within 4Å: Chain F: C.262, C.265, C.284, S.286, 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.20: 5 residues within 4Å: Chain G: C.341, C.344, S.346, C.364, C.367 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.341, G:C.344, G:C.364, G:C.367 ZN.25: 4 residues within 4Å: Chain I: C.349, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.349, I:C.352, I:C.371, I:C.376 ZN.29: 4 residues within 4Å: Chain J: C.183, C.186, C.211, C.236 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.183, J:C.186, J:C.211, J:C.236 ZN.31: 4 residues within 4Å: Chain K: C.311, C.314, C.333, C.338 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.311, K:C.314, K:C.333, K:C.338 ZN.34: 5 residues within 4Å: Chain L: C.262, C.265, C.284, S.286, C.289 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.262, L:C.265, L:C.284, L:C.289 ZN.36: 4 residues within 4Å: Chain N: C.661, C.664, H.674, H.680 4 PLIP interactions: 4 interactions with chain N Metal complexes: N:C.661, N:C.664, N:H.674, N:H.680

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

ADP.4: 14 residues within 4Å: Chain B: S.370, I.371, Y.372, H.374, S.412, T.413, A.414, K.415, S.416, Q.417 Chain D: I.650, R.651, E.654 Ligands: MG.5 13 PLIP interactions: 2 interactions with chain D, 11 interactions with chain B Salt bridges: D:R.651, D:R.651, B:K.415 Hydrogen bonds: B:Y.372, B:Y.372, B:S.412, B:T.413, B:T.413, B:T.413, B:A.414, B:K.415, B:S.416, B:Q.417 ADP.21: 16 residues within 4Å: Chain H: S.370, I.371, Y.372, P.411, S.412, T.413, A.414, K.415, S.416, Q.417, V.565 Chain J: L.406, I.650, R.651, E.654 Ligands: MG.22 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain J Hydrogen bonds: H:Y.372, H:Y.372, H:S.412, H:T.413, H:T.413, H:A.414, H:K.415, H:S.416, H:Q.417 Salt bridges: H:K.415, J:R.651, J:R.651

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cheng, J. et al., Structural Insight into the MCM double hexamer activation by Dbf4-Cdc7 kinase. Nat Commun (2022)

Release Date

2022-04-13

Peptides

DNA replication licensing factor MCM2: AG
DNA replication licensing factor MCM3: BH
DNA replication licensing factor MCM4: CI
Minichromosome maintenance protein 5: DJ
DNA replication licensing factor MCM6: EK
DNA replication licensing factor MCM7: FL
Cell division control protein 7: M
DDK kinase regulatory subunit DBF4: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

G
B

B
3

H
C

C
4

I
D

D
5

J
E

E
6

K
F

F
7

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

Cell division control protein 7

DDK kinase regulatory subunit DBF4

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