SMTL ID : 5bk4.1

Cryo-EM structure of Mcm2-7 double hexamer on dsDNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ADP.1: 9 residues within 4Å: Chain A: D.544, P.545, G.546, T.547, A.548, K.549, S.550, E.608, L.695 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.546, A:S.550, A:E.608 ADP.2: 11 residues within 4Å: Chain B: S.370, Y.372, P.411, S.412, T.413, A.414, K.415, S.416, Q.417 Chain D: I.650, R.651 11 PLIP interactions: 2 interactions with chain D, 9 interactions with chain B Salt bridges: D:R.651, D:R.651 Hydrogen bonds: B:Y.372, B:Y.372, B:S.412, B:T.413, B:A.414, B:K.415, B:S.416, B:S.416, B:Q.417 ADP.3: 14 residues within 4Å: Chain A: R.676, V.807, R.808 Chain D: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, I.568 12 PLIP interactions: 11 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:S.423, D:S.423, D:S.423, D:Q.424 Salt bridges: D:K.422, D:K.422, A:R.676 ADP.4: 12 residues within 4Å: Chain B: E.491, R.542, R.700, E.703 Chain F: I.422, Y.423, P.462, G.463, A.465, K.466, S.467, Q.468 13 PLIP interactions: 4 interactions with chain B, 9 interactions with chain F Hydrogen bonds: B:E.491, B:E.491, B:R.700, F:Y.423, F:Y.423, F:P.462, F:P.462, F:A.465, F:K.466, F:S.467, F:S.467, F:Q.468 Salt bridges: B:R.542 ADP.5: 7 residues within 4Å: Chain G: G.546, T.547, A.548, K.549, S.550, E.608, L.695 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.550, G:E.608, G:E.608 ADP.6: 11 residues within 4Å: Chain H: S.370, Y.372, P.411, S.412, T.413, A.414, K.415, S.416, Q.417 Chain J: I.650, R.651 12 PLIP interactions: 2 interactions with chain J, 10 interactions with chain H Salt bridges: J:R.651, J:R.651 Hydrogen bonds: H:Y.372, H:Y.372, H:S.412, H:T.413, H:A.414, H:K.415, H:S.416, H:S.416, H:S.416, H:Q.417 ADP.7: 13 residues within 4Å: Chain G: R.676, V.807 Chain J: S.377, I.378, F.379, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, I.568 12 PLIP interactions: 11 interactions with chain J, 1 interactions with chain G Hydrogen bonds: J:F.379, J:F.379, J:G.419, J:T.420, J:A.421, J:S.423, J:S.423, J:S.423, J:Q.424 Salt bridges: J:K.422, J:K.422, G:R.676 ADP.8: 12 residues within 4Å: Chain H: E.491, R.542, R.700, E.703 Chain L: I.422, Y.423, P.462, G.463, A.465, K.466, S.467, Q.468 13 PLIP interactions: 4 interactions with chain H, 9 interactions with chain L Hydrogen bonds: H:E.491, H:E.491, H:R.700, L:Y.423, L:Y.423, L:P.462, L:P.462, L:A.465, L:K.466, L:S.467, L:S.467, L:Q.468 Salt bridges: H:R.542

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noguchi, Y. et al., Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-10-25

Peptides

DNA replication licensing factor MCM2: AG
DNA replication licensing factor MCM3: BH
DNA replication licensing factor MCM4: CI
DNA replication licensing factor MCM5: DJ
DNA replication licensing factor MCM6: EK
DNA replication licensing factor MCM7: FL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

G
A

B
3

H
B

C
4

I
C

D
5

J
D

E
6

K
E

F
7

L
F

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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