SMTL ID : 8w0f.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

10 x ZN: ZINC ION

ZN.1: 7 residues within 4Å: Chain A: C.329, C.332, F.334, C.352, E.354, 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: 7 residues within 4Å: Chain C: C.309, V.311, C.312, H.314, C.331, R.333, C.334 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, C.207 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.172, D:C.175, D:C.197, D:C.207 ZN.10: 8 residues within 4Å: Chain E: C.158, D.160, C.161, T.163, C.180, N.182, C.185, N.187 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.158, E:C.161, E:C.180, E:C.185 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 ZN.16: 8 residues within 4Å: Chain G: C.329, K.331, C.332, F.334, C.352, E.354, C.355, S.357 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.329, G:C.332, G:C.352, G:C.355 ZN.21: 8 residues within 4Å: Chain I: C.309, V.311, C.312, H.314, C.331, R.333, C.334, S.339 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.309, I:C.312, I:C.331, I:C.334 ZN.22: 6 residues within 4Å: Chain J: C.172, S.174, C.175, C.197, T.199, C.207 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.172, J:C.175, J:C.197, J:C.207 ZN.25: 8 residues within 4Å: Chain K: C.158, D.160, C.161, T.163, C.180, N.182, C.185, N.187 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:C.158, K:C.161, K:C.180, K:C.185 ZN.28: 8 residues within 4Å: Chain L: C.184, Q.186, C.187, G.188, C.206, S.208, C.211, G.218 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.184, L:C.187, L:C.206, L:C.211

10 x MG: MAGNESIUM ION

MG.2: 4 residues within 4Å: Chain A: S.530, D.587, E.588 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.530 MG.4: 5 residues within 4Å: Chain B: S.354 Chain D: Q.464, R.513, R.611 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.354 MG.8: 4 residues within 4Å: Chain D: S.388, D.445, E.446 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.388 MG.11: 5 residues within 4Å: Chain C: R.646 Chain E: S.403, D.460, E.461 Ligands: ADP.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.403 MG.14: 5 residues within 4Å: Chain B: R.480 Chain F: K.387, S.388, D.445 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.388 MG.17: 4 residues within 4Å: Chain G: K.529, S.530 Chain K: R.619 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.530 MG.19: 5 residues within 4Å: Chain H: S.354, D.411, E.412 Chain J: R.513 Ligands: ADP.20 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.354 MG.23: 5 residues within 4Å: Chain G: E.605 Chain J: S.388, D.445, E.446 Ligands: ADP.24 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain J Metal complexes: G:E.605, J:S.388 MG.26: 6 residues within 4Å: Chain I: E.595, R.646 Chain K: S.403, D.460, E.461 Ligands: ADP.27 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.403 MG.29: 4 residues within 4Å: Chain H: R.480 Chain L: S.388, D.445 Ligands: ADP.30 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:S.388

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.3: 21 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: S.528, R.529, V.618, R.619, E.622 Ligands: MG.2 18 PLIP interactions: 13 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:Y.486, A:Y.486, A:G.526, A:T.527, A:T.527, A:A.528, A:K.529, A:S.530, A:S.530, A:Q.531, A:N.631, E:S.528, E:E.622 Salt bridges: A:K.529, A:K.529, E:R.619, E:R.619, E:R.619 ATP.18: 20 residues within 4Å: Chain G: 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 K: R.529, V.618, R.619, E.622 Ligands: MG.17 17 PLIP interactions: 14 interactions with chain G, 3 interactions with chain K Hydrogen bonds: G:Y.486, G:Y.486, G:H.488, G:G.526, G:T.527, G:T.527, G:A.528, G:K.529, G:S.530, G:Q.531, G:Q.531, G:N.631 Salt bridges: G:K.529, G:K.529, K:R.619, K:R.619, K:R.619

8 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.5: 21 residues within 4Å: Chain B: S.308, I.309, H.310, H.312, P.349, S.350, V.351, A.352, K.353, S.354, Q.355, I.499, H.502, V.503 Chain D: R.371, E.463, Q.464, V.610, R.611, E.614 Ligands: MG.4 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain D Hydrogen bonds: B:H.310, B:H.310, B:H.312, B:S.350, 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:R.371, D:R.371, D:E.463 Salt bridges: B:K.353, D:R.611, D:R.611 ADP.9: 23 residues within 4Å: Chain A: H.511, V.513, R.656, V.764, R.765, E.768 Chain D: S.342, I.343, F.344, D.382, P.383, G.384, T.385, A.386, K.387, S.388, Q.389, K.392, L.532, H.535, V.536, L.539 Ligands: MG.8 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain D Hydrogen bonds: A:H.511, A:R.656, D:F.344, D:F.344, D:D.382, D:K.387, D:S.388, D:Q.389 Salt bridges: D:K.387, D:K.392 ADP.12: 22 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, D.397, P.398, S.399, T.400, A.401, K.402, S.403, Q.404, I.548, R.551, I.552 Ligands: MG.11 15 PLIP interactions: 4 interactions with chain C, 11 interactions with chain E Hydrogen bonds: C:R.500, C:R.646, E:H.359, E:H.359, E:S.399, 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: 22 residues within 4Å: Chain B: I.337, E.429, R.480, A.617, R.618, E.621 Chain F: E.343, I.344, Y.345, G.346, 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 13 PLIP interactions: 10 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, F:Q.389, B:R.480, B:R.618 Salt bridges: F:K.387, B:R.618 ADP.20: 23 residues within 4Å: Chain H: S.308, I.309, H.310, H.312, D.348, P.349, S.350, V.351, A.352, K.353, S.354, Q.355, I.499, H.502, V.503 Chain J: R.371, E.463, Q.464, R.513, V.610, R.611, E.614 Ligands: MG.19 16 PLIP interactions: 10 interactions with chain H, 6 interactions with chain J Hydrogen bonds: H:H.310, H:H.310, H:S.350, H:V.351, H:A.352, H:K.353, H:S.354, H:S.354, H:Q.355, J:R.371, J:Q.464, J:R.513 Salt bridges: H:K.353, J:R.513, J:R.611, J:R.611 ADP.24: 20 residues within 4Å: Chain G: H.511, V.513, R.656, V.764, R.765, E.768 Chain J: S.342, I.343, F.344, P.383, G.384, T.385, A.386, K.387, S.388, Q.389, L.532, V.536, L.539 Ligands: MG.23 12 PLIP interactions: 9 interactions with chain J, 3 interactions with chain G Hydrogen bonds: J:F.344, J:F.344, J:D.382, J:A.386, J:K.387, J:S.388, J:Q.389, J:Q.389, G:H.511, G:E.605 Salt bridges: J:K.387, G:R.656 ADP.27: 20 residues within 4Å: Chain I: R.500, R.646, P.734, R.735, E.738 Chain K: 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.26 18 PLIP interactions: 13 interactions with chain K, 5 interactions with chain I Hydrogen bonds: K:H.359, K:H.359, K:N.361, K:S.399, K:T.400, K:T.400, K:A.401, K:K.402, K:S.403, K:Q.404, K:Q.404, K:Q.404, I:R.500, I:R.500, I:E.738 Salt bridges: K:K.402, I:R.735, I:R.735 ADP.30: 21 residues within 4Å: Chain H: I.337, E.429, Q.430, A.617, R.618, E.621 Chain L: E.343, I.344, Y.345, H.347, D.382, P.383, G.384, V.385, A.386, K.387, S.388, Q.389, L.533, I.537 Ligands: MG.29 13 PLIP interactions: 11 interactions with chain L, 2 interactions with chain H Hydrogen bonds: L:Y.345, L:Y.345, L:G.384, L:V.385, L:A.386, L:K.387, L:S.388, L:S.388, L:Q.389, L:Q.389 Salt bridges: L:K.387, H:R.618, H:R.618

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, R. et al., Multiple mechanisms for licensing human replication origins. Nature (2024)

Release Date

2024-10-02

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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