SMTL ID : 9caq.1

Cryo-EM structure of a human MCM2-7 double hexamer formed from independently loaded MCM2-7 single hexamers

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, K.331, C.332, F.334, C.352, E.354, C.355 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.329, A:C.332, A:C.352, A:C.355 ZN.5: 7 residues within 4Å: Chain C: C.306, V.308, C.309, H.311, C.328, C.331, S.336 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.306, C:C.309, C:C.328, C:C.331 ZN.7: 6 residues within 4Å: Chain D: C.175, S.177, C.178, C.200, T.202, C.210 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:C.175, D:S.177, D:C.178, D:C.200, D:C.210 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.12: 5 residues within 4Å: Chain F: C.187, C.190, C.209, S.211, C.214 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:C.187, F:C.190, F:C.209, F:S.211, F:C.214 ZN.15: 7 residues within 4Å: Chain G: C.329, K.331, C.332, F.334, C.352, 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.19: 8 residues within 4Å: Chain I: C.306, V.308, C.309, H.311, C.328, R.330, C.331, S.336 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.306, I:C.309, I:C.328, I:C.331 ZN.21: 6 residues within 4Å: Chain J: C.175, S.177, C.178, C.200, T.202, C.210 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:C.175, J:C.178, J:C.200, J:C.210 ZN.24: 7 residues within 4Å: Chain K: C.158, D.160, C.161, 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.27: 6 residues within 4Å: Chain L: C.187, C.190, G.191, C.209, S.211, C.214 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:C.187, L:C.190, L:C.209, L:S.211, L:C.214

9 x MG: MAGNESIUM ION

MG.2: 5 residues within 4Å: Chain A: K.529, S.530, D.587, E.588 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.530 MG.8: 5 residues within 4Å: Chain A: E.605 Chain D: S.391, D.448, E.449 Ligands: ADP.9 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.391 MG.11: 5 residues within 4Å: Chain C: E.592, R.643 Chain E: S.403, E.461 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.403 MG.13: 7 residues within 4Å: Chain B: H.423, R.478 Chain F: K.390, S.391, D.448, E.449 Ligands: ADP.14 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.391 MG.16: 4 residues within 4Å: Chain G: S.530, D.587 Chain K: R.529 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:S.530 MG.20: 7 residues within 4Å: Chain H: K.351, S.352, D.409, E.410 Chain J: E.463, R.516 Ligands: ADP.18 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain J Metal complexes: H:S.352, J:E.463 MG.22: 4 residues within 4Å: Chain G: E.605 Chain J: S.391, D.448 Ligands: ADP.23 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:S.391 MG.25: 5 residues within 4Å: Chain I: E.592 Chain K: S.403, D.460, E.461 Ligands: ADP.26 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:S.403 MG.28: 4 residues within 4Å: Chain L: S.391, D.448, E.449 Ligands: ADP.29 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:S.391, L:D.448, L:E.449

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.3: 21 residues within 4Å: Chain A: S.484, I.485, Y.486, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, E.588, N.631, L.675, F.678, V.679 Chain E: P.525, R.529, V.618, R.619, E.622 Ligands: MG.2 20 PLIP interactions: 14 interactions with chain A, 6 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:Q.531, A:Q.531, A:E.588, A:N.631, E:R.529, E:E.622, E:E.622 Salt bridges: A:K.529, A:K.529, E:R.619, E:R.619, E:R.619 ATP.17: 21 residues within 4Å: Chain G: I.485, Y.486, G.487, H.488, P.525, G.526, T.527, A.528, K.529, S.530, Q.531, E.588, N.631, L.675, F.678, V.679 Chain K: L.386, R.529, V.618, R.619 Ligands: MG.16 17 PLIP interactions: 14 interactions with chain G, 3 interactions with chain K Hydrogen bonds: G:Y.486, G:Y.486, G:G.526, G:T.527, G:A.528, G:K.529, G:S.530, G:Q.531, G:Q.531, G:E.588, G:N.631, 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.4: 19 residues within 4Å: Chain B: I.307, H.308, H.310, P.347, S.348, V.349, A.350, K.351, S.352, Q.353, I.497, V.501 Chain D: R.374, E.466, Q.467, R.516, V.613, R.614, E.617 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:H.308, B:H.308, B:S.348, B:V.349, B:A.350, B:K.351, B:S.352, B:S.352, B:Q.353, B:Q.353, D:R.374 Salt bridges: D:R.516, D:R.614, D:R.614 ADP.6: 20 residues within 4Å: Chain C: R.497, E.592, R.643, P.731, R.732, E.735 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, I.552 Ligands: MG.11 17 PLIP interactions: 5 interactions with chain C, 12 interactions with chain E Hydrogen bonds: C:R.497, C:E.592, 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:S.403, E:Q.404, E:Q.404 Salt bridges: C:R.643, C:R.732, C:R.732, E:K.402 ADP.9: 21 residues within 4Å: Chain A: H.511, K.512, V.513, V.764, R.765, E.768 Chain D: I.346, F.347, D.385, P.386, G.387, T.388, A.389, K.390, S.391, Q.392, L.535, H.538, V.539, L.542 Ligands: MG.8 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain D Salt bridges: A:R.765, D:K.390 Hydrogen bonds: D:F.347, D:F.347, D:D.385, D:K.390, D:S.391, D:Q.392, D:Q.392 ADP.14: 23 residues within 4Å: Chain B: I.335, H.423, E.427, Q.428, R.478, A.615, R.616, E.619 Chain F: E.346, I.347, Y.348, H.350, P.386, G.387, V.388, A.389, K.390, S.391, Q.392, L.536, H.539, I.540 Ligands: MG.13 15 PLIP interactions: 5 interactions with chain B, 10 interactions with chain F Hydrogen bonds: B:E.427, F:Y.348, F:Y.348, F:G.387, F:A.389, F:K.390, F:S.391, F:S.391, F:Q.392, F:Q.392 Salt bridges: B:H.423, B:R.478, B:R.616, B:R.616, F:K.390 ADP.18: 23 residues within 4Å: Chain H: S.306, I.307, H.308, D.346, P.347, S.348, V.349, A.350, K.351, S.352, Q.353, N.453, I.497, H.500, V.501 Chain J: R.374, E.466, Q.467, R.516, V.613, R.614, E.617 Ligands: MG.20 13 PLIP interactions: 9 interactions with chain H, 4 interactions with chain J Hydrogen bonds: H:H.308, H:H.308, H:S.348, H:V.349, H:A.350, H:K.351, H:S.352, H:Q.353, J:Q.467 Salt bridges: H:K.351, J:R.516, J:R.614, J:R.614 ADP.23: 22 residues within 4Å: Chain G: H.511, V.513, S.655, R.656, V.764, R.765, E.768, R.772 Chain J: S.345, I.346, F.347, P.386, G.387, T.388, A.389, K.390, S.391, Q.392, L.535, H.538, V.539 Ligands: MG.22 7 PLIP interactions: 5 interactions with chain J, 2 interactions with chain G Hydrogen bonds: J:F.347, J:K.390, J:S.391, J:Q.392, G:H.511 Salt bridges: J:K.390, G:R.656 ADP.26: 20 residues within 4Å: Chain I: R.497, P.731, R.732, E.735 Chain K: T.357, I.358, H.359, G.360, N.361, P.398, S.399, T.400, A.401, K.402, S.403, Q.404, I.548, R.551, I.552 Ligands: MG.25 14 PLIP interactions: 10 interactions with chain K, 4 interactions with chain I Hydrogen bonds: K:H.359, K:H.359, K:S.399, K:T.400, K:A.401, K:K.402, K:S.403, K:Q.404, K:Q.404, I:R.497, I:R.732, I:E.735 Salt bridges: K:K.402, I:R.732 ADP.29: 21 residues within 4Å: Chain H: I.335, E.427, Q.428, R.478, A.615, R.616, E.619 Chain L: E.346, I.347, Y.348, P.386, G.387, V.388, A.389, K.390, S.391, Q.392, L.536, H.539, I.540 Ligands: MG.28 14 PLIP interactions: 12 interactions with chain L, 2 interactions with chain H Hydrogen bonds: L:Y.348, L:G.387, L:V.388, L:A.389, L:K.390, L:S.391, L:S.391, L:S.391, L:Q.392, L:Q.392, L:H.539 Salt bridges: L:K.390, H:R.616, H:R.616

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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