SMTL ID : 9i3i.1

Cryo-EM structure of the MCM-ORC (MO) complex featuring an ORC2 regulatory domain involved in cell cycle regulation of MCM-DH loading for DNA replication.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 22 residues within 4Å: Chain A: S.467, L.484, A.486, R.487, P.516, G.517, V.518, G.519, K.520, T.521, L.522, Y.662, I.670, R.674, A.738, R.739, L.742 Chain D: Y.232, R.263, S.266, R.267 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:G.517, A:G.519, A:K.520, A:T.521, A:L.522, A:Y.662, A:R.674, A:R.674, A:R.739, A:R.739 Salt bridges: A:K.520, A:K.520, A:R.739, A:R.739, A:R.739, D:R.267 ATP.3: 17 residues within 4Å: Chain D: Y.61, G.62, T.63, P.103, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, E.218, C.250, T.251, P.335, K.338 Ligands: MG.4 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Q.105, D:Q.105, D:S.106, D:Y.107, D:K.108, D:T.109, D:T.109, D:Y.110, D:E.218, D:E.218, D:K.338 Salt bridges: D:K.108, D:K.108 ATP.5: 22 residues within 4Å: Chain E: V.8, A.9, F.10, R.11, Y.38, S.39, G.40, T.41, G.42, K.43, T.44, Y.45, K.49, D.133, L.171, Y.192, I.200, M.203, S.204, I.255, F.256 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.40, E:T.41, E:G.42, E:K.43, E:T.44, E:T.44, E:T.44, E:Y.45, E:K.49, E:Y.192, E:Y.192, E:S.204 Salt bridges: E:K.43, E:K.43

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.521 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain D: K.108, T.109, C.250 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.109 MG.6: 3 residues within 4Å: Chain E: K.43, T.44 Ligands: ATP.5 No protein-ligand interaction detected (PLIP)

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

ADP.7: 14 residues within 4Å: Chain G: I.505, G.507, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, E.608, N.651, L.695, V.699 Chain K: R.798 6 PLIP interactions: 5 interactions with chain G, 1 interactions with chain K Hydrogen bonds: G:K.549, G:S.550, G:E.608, G:E.608, G:N.651 Salt bridges: K:R.798 ADP.9: 20 residues within 4Å: Chain H: I.406, Y.407, G.408, H.409, P.446, S.447, T.448, A.449, K.450, S.451, Q.452, I.596, V.600 Chain J: M.404, L.406, R.407, E.498, R.549, I.650, R.651 12 PLIP interactions: 8 interactions with chain H, 4 interactions with chain J Hydrogen bonds: H:Y.407, H:Y.407, H:T.448, H:T.448, H:S.451, H:S.451, H:Q.452, J:R.407 Salt bridges: H:K.450, J:R.549, J:R.651, J:R.651 ADP.11: 17 residues within 4Å: Chain G: H.531, V.807, R.808, E.811 Chain J: S.377, I.378, F.379, N.381, P.418, G.419, T.420, A.421, K.422, S.423, Q.424, I.568, V.572 11 PLIP interactions: 11 interactions with chain J Hydrogen bonds: J:F.379, J:F.379, J:G.419, J:G.419, J:A.421, J:S.423, J:S.423, J:Q.424, J:Q.424, J:Q.424 Salt bridges: J:K.422 ADP.14: 19 residues within 4Å: Chain H: L.434, E.526, Q.527, R.577, R.735 Chain L: I.422, Y.423, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, E.525, N.568, L.612, V.616, V.619 8 PLIP interactions: 1 interactions with chain H, 7 interactions with chain L Salt bridges: H:R.577 Hydrogen bonds: L:Y.423, L:A.465, L:K.466, L:S.467, L:Q.468, L:Q.468, L:E.525

5 x ZN: ZINC ION(Non-covalent)

ZN.8: 6 residues within 4Å: Chain G: K.343, C.344, C.364, N.366, C.367, S.369 No protein-ligand interaction detected (PLIP) ZN.10: 5 residues within 4Å: Chain I: C.349, V.351, C.352, C.371, C.376 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:C.349, I:C.352, I:C.371, I:C.376 ZN.12: 6 residues within 4Å: Chain J: C.183, C.186, H.188, C.211, C.236, P.240 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:C.183, J:C.186, J:C.211 ZN.13: 5 residues within 4Å: Chain K: C.311, C.314, C.333, N.335, C.338 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:C.311, K:C.333, K:C.338 ZN.15: 5 residues within 4Å: Chain L: C.262, C.265, C.284, S.286, C.289 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:C.262, L:C.265, L:C.284, L:C.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miller, T.C.R. et al., Cell Cycle Regulation has Shaped Budding Yeast Replication Origin Structure and Function. To Be Published

Release Date

2025-06-25

Peptides

Origin recognition complex subunit 1: A
Origin recognition complex subunit 2: B
Origin recognition complex subunit 3: C
Origin recognition complex subunit 4: D
Origin recognition complex subunit 5: E
Origin recognition complex subunit 6: F
DNA replication licensing factor MCM2: G
DNA replication licensing factor MCM3: H
DNA replication licensing factor MCM4: I
Minichromosome maintenance protein 5: J
DNA replication licensing factor MCM6: K
DNA replication licensing factor MCM7: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
2

H
3

I
4

J
5

K
6

L
7

Origin recognition complex subunit 1

Origin recognition complex subunit 2

Origin recognition complex subunit 3

Origin recognition complex subunit 4

Origin recognition complex subunit 5

Origin recognition complex subunit 6

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

Minichromosome maintenance protein 5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

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