SMTL ID : 8b9a.1

S. cerevisiae replisome + Ctf4, bound by pol alpha primase. Complex engaged with a fork DNA substrate containing a 60 nucleotide lagging strand.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-3-mer

Ligands

4 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 19 residues within 4Å: Chain A: S.504, I.505, Y.506, P.545, G.546, T.547, A.548, K.549, S.550, Q.551, E.608, N.651, L.695, V.699 Chain E: R.708, V.797, R.798, E.801 Ligands: MG.2 18 PLIP interactions: 6 interactions with chain E, 12 interactions with chain A Hydrogen bonds: E:R.708, E:R.708, E:R.798, E:R.798, E:E.801, E:E.801, A:Y.506, A:G.546, A:A.548, A:K.549, A:K.549, A:S.550, A:S.550, A:Q.551, A:Q.551, A:E.608, A:E.608, A:N.651 ANP.3: 18 residues within 4Å: Chain B: I.409, Y.410, P.449, S.450, T.451, A.452, K.453, S.454, Q.455, N.555, I.599, V.603 Chain D: E.498, R.549, I.650, R.651, E.654 Ligands: MG.7 12 PLIP interactions: 4 interactions with chain D, 8 interactions with chain B Hydrogen bonds: D:R.651, D:R.651, D:E.654, D:E.654, B:Y.410, B:Y.410, B:S.450, B:A.452, B:K.453, B:K.453, B:S.454, B:Q.455 ANP.4: 25 residues within 4Å: Chain C: S.529, I.530, Y.531, L.533, D.569, P.570, S.571, T.572, S.573, K.574, S.575, Q.576, N.676, L.720, H.723, L.724 Chain F: M.448, I.450, E.542, A.589, R.593, P.686, R.687, L.690 Ligands: MG.5 16 PLIP interactions: 11 interactions with chain C, 5 interactions with chain F Hydrogen bonds: C:Y.531, C:Y.531, C:S.571, C:S.571, C:T.572, C:S.573, C:K.574, C:K.574, C:S.575, C:Q.576, C:N.676, F:R.593, F:R.593, F:R.687, F:R.687 Salt bridges: F:R.687 ANP.10: 24 residues within 4Å: Chain B: L.437, E.529, Q.530, S.576, R.580, A.737, R.738, E.741 Chain F: E.421, I.422, Y.423, N.425, D.461, P.462, G.463, V.464, A.465, K.466, S.467, Q.468, N.568, L.612, V.616 Ligands: MG.11 19 PLIP interactions: 7 interactions with chain B, 12 interactions with chain F Hydrogen bonds: B:Q.530, B:R.580, B:R.580, B:R.738, B:R.738, B:E.741, F:Y.423, F:Y.423, F:N.425, F:G.463, F:V.464, F:A.465, F:K.466, F:K.466, F:S.467, F:Q.468, F:N.568, F:N.568 Salt bridges: B:R.738

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: K.549, S.550 Ligands: ANP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.550 MG.5: 4 residues within 4Å: Chain C: S.575 Chain F: R.593, R.687 Ligands: ANP.4 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain B: S.454 Chain D: E.498, R.651 Ligands: ANP.3 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.498, D:E.498 MG.11: 3 residues within 4Å: Chain B: R.580 Chain F: S.467 Ligands: ANP.10 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:S.467

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 7 residues within 4Å: Chain C: C.349, V.351, C.352, H.354, C.371, R.373, C.376 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.349, C:C.352, C:C.371, C:C.376 ZN.8: 6 residues within 4Å: Chain D: C.183, C.186, H.188, L.212, S.213, C.236 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.186, D:L.212, D:S.213, D:C.236 ZN.9: 6 residues within 4Å: Chain E: C.311, M.313, C.314, C.333, C.338, N.340 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.311, E:C.314, E:C.333, E:C.338 ZN.12: 5 residues within 4Å: Chain F: C.262, C.265, Y.267, C.284, C.289 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.262, F:C.265, F:C.284, F:C.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, M.L. et al., How Pol alpha-primase is targeted to replisomes to prime eukaryotic DNA replication. Mol.Cell (2023)

Release Date

2023-08-09

Peptides

DNA replication licensing factor MCM2: A
DNA replication licensing factor MCM3: B
DNA replication licensing factor MCM4: C
Minichromosome maintenance protein 5: D
DNA replication licensing factor MCM6: E
DNA replication licensing factor MCM7: F
DNA primase large subunit: G
DNA polymerase alpha subunit B: H
DNA replication complex GINS protein PSF1: I
DNA replication complex GINS protein PSF2: J
DNA replication complex GINS protein PSF3: K
DNA replication complex GINS protein SLD5: L
Cell division control protein 45: M
DNA polymerase alpha catalytic subunit A: N
Mediator of replication checkpoint protein 1: O
DNA primase small subunit: R
Topoisomerase 1-associated factor 1: S
Chromosome segregation in meiosis protein 3: T
DNA polymerase alpha-binding protein: UVW

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
2

B
3

C
4

D
5

E
6

F
7

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
J

O
P

R
S

S
X

T
Y

U
H

V
L

W
K

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

DNA primase large subunit

DNA polymerase alpha subunit B

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 alpha catalytic subunit A

Mediator of replication checkpoint protein 1

DNA primase small subunit

Topoisomerase 1-associated factor 1

Chromosome segregation in meiosis protein 3

DNA polymerase alpha-binding protein

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