SMTL ID : 8w0i.1

Cryo-EM structure of the human MCM2-7 heterohexamer

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, C.332, F.334, 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: 7 residues within 4Å: Chain C: C.309, V.311, C.312, H.314, C.331, C.334, T.336 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.309, C:C.312, C:C.331, C:C.334 ZN.9: 6 residues within 4Å: Chain D: C.172, C.175, N.177, C.197, P.208, Y.212 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, C.180, 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

5 x MG: MAGNESIUM ION

MG.2: 4 residues within 4Å: Chain A: S.530, D.587 Chain E: R.529 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.530 MG.4: 2 residues within 4Å: Chain B: S.354 Ligands: ADP.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.354 MG.7: 3 residues within 4Å: Chain C: K.519, S.520 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.520 MG.11: 6 residues within 4Å: Chain C: E.595, R.646, R.735 Chain E: S.403, D.460 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.403 MG.14: 4 residues within 4Å: Chain B: R.618 Chain F: S.388, D.445 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.388

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE

ATP.3: 23 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, E.588, N.631, Q.671, L.675, F.678, V.679 Chain E: S.528, R.529, V.618, R.619, E.622 Ligands: MG.2 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain E Hydrogen bonds: A:Y.486, A:Y.486, A:H.488, A:G.526, A:A.528, A:K.529, A:S.530, A:S.530, A:S.530, A:Q.531, A:E.588, A:N.631, E:E.622 Salt bridges: A:K.529, A:K.529, E:R.529, E:R.619, E:R.619, E:R.619 ATP.8: 25 residues within 4Å: Chain C: S.472, I.473, Y.474, E.475, H.476, D.514, P.515, G.516, T.517, S.518, K.519, S.520, Q.521, E.578, N.621, Y.661, L.665, H.668, L.669 Chain F: R.514, S.602, A.603, R.604, L.607 Ligands: MG.7 19 PLIP interactions: 15 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:Y.474, C:Y.474, C:H.476, C:D.514, C:G.516, C:T.517, C:T.517, C:S.518, C:S.518, C:S.518, C:K.519, C:S.520, C:Q.521 Salt bridges: C:K.519, C:K.519, F:R.514, F:R.604, F:R.604, F:R.604 ATP.12: 21 residues within 4Å: Chain C: R.500, R.646, P.734, R.735, E.738 Chain E: I.358, H.359, N.361, D.397, P.398, S.399, T.400, A.401, K.402, S.403, Q.404, N.504, I.548, R.551, I.552 Ligands: MG.11 19 PLIP interactions: 13 interactions with chain E, 6 interactions with chain C Hydrogen bonds: 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:S.403, E:Q.404, E:N.504, C:R.500, C:E.738 Salt bridges: E:K.402, E:K.402, C:R.646, C:R.735, C:R.735, C:R.735 ATP.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, H.347, P.383, G.384, V.385, A.386, K.387, S.388, Q.389, N.489, L.533, H.536, I.537 Ligands: MG.14 14 PLIP interactions: 10 interactions with chain F, 4 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:N.489, B:E.621 Salt bridges: F:K.387, B:R.618, B:R.618, B:R.618

1 x ADP: ADENOSINE-5'-DIPHOSPHATE

ADP.5: 20 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, V.610, R.611, E.614 Ligands: MG.4 15 PLIP interactions: 4 interactions with chain D, 11 interactions with chain B Hydrogen bonds: D:R.371, D:E.614, B:H.310, B:H.310, B:H.312, B:S.350, B:V.351, B:A.352, B:S.354, B:S.354, B:Q.355 Salt bridges: D:R.611, D:R.611, B:K.353, B:K.353

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: 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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