SMTL ID : 8w0e.1

Cryo-EM structure of a human MCM2-7 single hexamer on dsDNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

5 x ZN: ZINC ION

ZN.1: 6 residues within 4Å: Chain A: C.329, K.331, C.332, C.352, C.355, S.357 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.329, A:C.332, A:C.352, A:C.355 ZN.6: 8 residues within 4Å: Chain C: C.309, V.311, C.312, C.331, R.333, C.334, T.336, S.339 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.309, C:C.312, C:C.331, C:C.334 ZN.7: 5 residues within 4Å: Chain D: C.172, S.174, C.175, C.197, P.211 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.172, D:C.175, D:C.197 ZN.10: 6 residues within 4Å: Chain E: C.158, D.160, C.161, T.163, C.180, N.182 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.158, E:C.161, E:C.180 ZN.13: 7 residues within 4Å: Chain F: C.184, Q.186, C.187, C.206, S.208, C.211, G.218 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.184, F:C.187, F:C.206, F:C.211

5 x MG: MAGNESIUM ION

MG.2: 3 residues within 4Å: Chain A: S.530, D.587 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.530 MG.4: 5 residues within 4Å: Chain B: K.353, S.354, D.411 Chain D: R.513 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.354 MG.8: 4 residues within 4Å: Chain A: E.605 Chain D: S.388, D.445 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.388 MG.11: 4 residues within 4Å: Chain C: R.646 Chain E: S.403, E.461 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.461 MG.14: 3 residues within 4Å: Chain B: R.480 Chain F: S.388 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.388

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.3: 19 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, N.631, L.675, F.678, V.679 Chain E: V.618, R.619, E.622 Ligands: MG.2 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain E Hydrogen bonds: A:Y.486, A:Y.486, A:H.488, A:G.526, A:T.527, A:T.527, A:A.528, A:K.529, A:S.530, A:Q.531, A:Q.531, A:N.631, E:E.622 Salt bridges: A:K.529, A:K.529, E:R.619, E:R.619, E:R.619

4 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.5: 23 residues within 4Å: Chain B: S.308, I.309, H.310, G.311, H.312, P.349, S.350, V.351, A.352, K.353, S.354, Q.355, N.455, I.499, H.502, V.503 Chain D: R.371, E.463, Q.464, V.610, R.611, E.614 Ligands: MG.4 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:H.310, B:H.310, B:S.350, B:V.351, B:A.352, B:K.353, B:S.354, B:S.354, B:Q.355, B:Q.355, D:E.463, D:Q.464 Salt bridges: B:K.353, D:R.611, D:R.611 ADP.9: 22 residues within 4Å: Chain A: H.511, E.605, 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, L.532, H.535, V.536, L.539 Ligands: MG.8 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:F.344, D:F.344, D:A.386, D:K.387, D:S.388, D:S.388, D:S.388, D:Q.389, A:H.511, A:R.656 Salt bridges: D:K.387 ADP.12: 21 residues within 4Å: Chain C: R.500, E.595, R.646, P.734, R.735, E.738 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.11 14 PLIP interactions: 3 interactions with chain C, 11 interactions with chain E Hydrogen bonds: C:R.500, 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:Q.404 Salt bridges: C:R.735, C:R.735, E:K.402 ADP.15: 20 residues within 4Å: Chain B: I.337, E.429, A.617, R.618, E.621 Chain F: E.343, I.344, Y.345, H.347, P.383, G.384, V.385, A.386, K.387, S.388, Q.389, L.533, H.536, I.537 Ligands: MG.14 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain B Hydrogen bonds: F:Y.345, F:Y.345, F:G.384, F:V.385, F:A.386, F:K.387, F:S.388, F:Q.389, B:E.621 Salt bridges: F:K.387, B:R.618, B:R.618

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, R. et al., Multiple pathways for licensing human replication origins. To Be Published

Release Date

2024-10-02

Peptides

DNA replication licensing factor MCM2: A
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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

DNA replication licensing factor MCM2

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

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