SMTL ID : 6hv9.1

S. cerevisiae CMG-Pol epsilon-DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x DT- DT- DT- DT- DT- DT- DT: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*T)-3')(Non-covalent)

DT-DT-DT-DT-DT-DT-DT.1: 10 residues within 4Å: Chain A: A.444, V.446, R.455, K.499, A.500 Chain C: V.453 Chain E: S.579, V.580, R.581, K.633 Protein-ligand interaction information (PLIP) not available

2 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Covalent)

AGS.2: 13 residues within 4Å: Chain C: D.417, P.418, G.419, T.420, A.421, K.422, S.423, N.524 Chain E: I.533, R.534, H.621, R.676, R.808 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain E Hydrogen bonds: C:G.419, C:T.420, C:A.421, C:K.422, C:S.423, C:S.423, C:N.524, E:I.533, E:R.534, E:R.534, E:H.621, E:R.676, E:R.676 Salt bridges: C:K.422 AGS.3: 15 residues within 4Å: Chain A: S.370, I.371, Y.372, P.411, S.412, A.414, K.415, S.416, E.474 Chain C: L.406, H.494, Q.499, R.549, I.650, R.651 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:H.494, A:Y.372, A:A.414, A:S.416, A:S.416, A:E.474 Salt bridges: C:R.549, C:R.651, C:R.651

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain O: C.801, C.804, C.823, C.826 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.801, O:C.804, O:C.823, O:C.826 ZN.5: 5 residues within 4Å: Chain O: C.857, R.859, C.860, C.872, C.874 4 PLIP interactions: 4 interactions with chain O Metal complexes: O:C.857, O:C.860, O:C.872, O:C.874

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goswami, P. et al., Structure of DNA-CMG-Pol epsilon elucidates the roles of the non-catalytic polymerase modules in the eukaryotic replisome. Nat Commun (2018)

Release Date

2018-12-12

Peptides

DNA replication licensing factor MCM3: A
DNA replication licensing factor MCM4: B
DNA replication licensing factor MCM5: C
DNA replication licensing factor MCM6: D
DNA replication licensing factor MCM2: E
DNA replication licensing factor MCM7: F
DNA replication complex GINS protein PSF1: G
DNA replication complex GINS protein PSF2: H
DNA replication complex GINS protein PSF3: I
DNA replication complex GINS protein SLD5: J
Cell division control protein 45: K
DNA polymerase epsilon subunit B: N
DNA polymerase epsilon catalytic subunit: O

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
3

B
4

C
5

D
6

E
2

F
7

G
C

H
D

I
E

J
F

K
G

N
B

O
A

DNA replication licensing factor MCM3

DNA replication licensing factor MCM4

DNA replication licensing factor MCM5

DNA replication licensing factor MCM6

DNA replication licensing factor MCM2

DNA replication licensing factor MCM7

DNA replication complex GINS protein PSF1

DNA replication complex GINS protein PSF2

DNA replication complex GINS protein PSF3

DNA replication complex GINS protein SLD5

Cell division control protein 45

DNA polymerase epsilon subunit B

DNA polymerase epsilon catalytic subunit

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