SMTL ID : 9bcx.1

Cryo-EM structure of the S. cerevisiae ORC-Cdc6-Mcm2-7-DNA complex with a fully closed Mcm2-Mcm5 DNA entry gate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 20 residues within 4Å: Chain G: S.432, L.449, P.450, P.481, G.482, V.483, G.484, K.485, T.486, L.487, Y.627, I.635, R.639, A.703, R.704 Chain J: H.240, R.263, S.266, R.267 Ligands: MG.2 16 PLIP interactions: 3 interactions with chain J, 13 interactions with chain G Hydrogen bonds: J:H.240, J:S.266, G:S.432, G:G.482, G:V.483, G:G.484, G:K.485, G:T.486, G:T.486, G:L.487, G:R.639 Salt bridges: J:R.267, G:K.485, G:K.485, G:R.704, G:R.704 ATP.3: 17 residues within 4Å: Chain J: Y.61, G.62, P.103, R.104, Q.105, S.106, Y.107, K.108, T.109, Y.110, D.113, E.218, P.335 Chain K: K.151, K.158, H.182 Ligands: MG.4 23 PLIP interactions: 19 interactions with chain J, 4 interactions with chain K Hydrogen bonds: J:Q.105, J:Q.105, J:Q.105, J:S.106, J:Y.107, J:K.108, J:T.109, J:T.109, J:Y.110, J:D.113, J:D.113, J:E.218, J:E.218, K:K.158 Salt bridges: J:R.104, J:K.108, J:K.108, K:K.151, K:K.151, K:H.182 pi-Stacking: J:Y.110, J:Y.110 pi-Cation interactions: J:K.69 ATP.5: 15 residues within 4Å: Chain K: A.9, Y.38, S.39, G.40, T.41, G.42, K.43, T.44, Y.45, L.171, Y.192, I.200, I.255, F.256 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:G.40, K:T.41, K:G.42, K:K.43, K:T.44, K:T.44, K:Y.45, K:Y.192, K:Y.192 Salt bridges: K:K.43, K:K.43 pi-Stacking: K:Y.45, K:Y.45

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain G: T.486, D.566, E.567 Chain J: R.267 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.486 MG.4: 2 residues within 4Å: Chain J: T.109 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.109 MG.6: 3 residues within 4Å: Chain K: T.44, D.133 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.44 MG.7: 3 residues within 4Å: Chain G: R.616 Chain M: T.115, R.332 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:T.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Faull, S.V. et al., MCM2-7 ring closure involves the Mcm5 C-terminus and triggers Mcm4 ATP hydrolysis. Nat Commun (2025)

Release Date

2025-01-01

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM5: C
DNA replication licensing factor MCM4: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F
Origin recognition complex subunit 1: G
Origin recognition complex subunit 2: H
Origin recognition complex subunit 3: I
Origin recognition complex subunit 4: J
Origin recognition complex subunit 5: K
Origin recognition complex subunit 6: L
Cell division control protein 6: M
TAH11 isoform 1: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
5

D
4

E
6

F
7

G
B

H
C

I
D

J
E

K
F

L
G

M
I

N
8

DNA replication licensing factor MCM2

DNA replication licensing factor MCM3

DNA replication licensing factor MCM5

DNA replication licensing factor MCM4

DNA replication licensing factor MCM6

DNA replication licensing factor MCM7

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

Cell division control protein 6

TAH11 isoform 1

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