SMTL ID : 8twa.1

Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA-PolE-DNA complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

1 x DT- DG- DT- DT- DG- DC- DT- DG- DC: Primer DNA(Non-covalent)

DT-DG-DT-DT-DG-DC-DT-DG-DC.1: 15 residues within 4Å: Chain B: A.6, G.7, C.8, A.9, G.10, C.11, A.12, A.13, C.14, A.15 Chain C: P.433, Q.434, G.435, R.988, W.1179 Protein-ligand interaction information (PLIP) not available

1 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 9 residues within 4Å: Chain C: D.664, C.665, C.668, F.670, N.671, C.677, A.678, C.763, R.765 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.665, C:C.668, C:C.677, C:C.763

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.3: 23 residues within 4Å: Chain F: V.9, R.13, P.14, D.19, I.20, V.21, G.22, M.47, P.48, G.49, I.50, G.51, K.52, T.53, T.54, N.142, R.171, M.199, R.200, I.203 Chain G: E.127, R.152 Ligands: MG.4 18 PLIP interactions: 17 interactions with chain F, 1 interactions with chain G Hydrogen bonds: F:V.9, F:R.13, F:R.13, F:V.21, F:M.47, F:G.49, F:I.50, F:I.50, F:G.51, F:K.52, F:T.53, F:T.54, F:R.200, F:R.200, G:R.152 Salt bridges: F:K.52, F:R.200, F:R.200 AGS.5: 22 residues within 4Å: Chain G: V.8, Y.11, R.12, P.13, E.18, V.19, Y.20, P.47, G.48, T.49, G.50, K.51, T.52, S.53, N.140, L.161, R.169, M.197, R.198, L.201 Chain H: R.170 Ligands: MG.6 22 PLIP interactions: 20 interactions with chain G, 2 interactions with chain H Hydrogen bonds: G:Y.11, G:R.12, G:R.12, G:Y.20, G:G.48, G:T.49, G:T.49, G:T.49, G:T.49, G:G.50, G:K.51, G:T.52, G:T.52, G:S.53, G:S.53, G:R.198, H:R.170, H:R.170 Salt bridges: G:R.12, G:K.51, G:R.198, G:R.198 AGS.7: 23 residues within 4Å: Chain H: V.15, Y.18, R.19, P.20, E.25, T.27, P.54, G.55, T.56, G.57, K.58, T.59, S.60, N.158, L.179, R.187, L.215, R.216, I.219 Chain I: E.159, P.180, R.184 Ligands: MG.8 20 PLIP interactions: 18 interactions with chain H, 2 interactions with chain I Hydrogen bonds: H:Y.18, H:R.19, H:T.27, H:G.55, H:T.56, H:T.56, H:T.56, H:G.57, H:K.58, H:T.59, H:S.60, H:S.60, H:R.216, H:R.216, I:R.184, I:R.184 Salt bridges: H:R.19, H:K.58, H:R.216, H:R.216

3 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain F: T.53 Chain G: E.127 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.53 MG.6: 4 residues within 4Å: Chain G: T.52, D.109 Chain H: R.170 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.52 MG.8: 5 residues within 4Å: Chain H: T.59, D.127, E.128 Chain I: R.184 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.59

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

ADP.9: 15 residues within 4Å: Chain I: V.5, R.9, P.10, L.16, S.17, H.18, G.46, G.48, K.49, K.50, T.51, L.230, R.231, L.234 Chain J: F.541 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:S.17, I:S.17, I:T.47, I:G.48, I:K.49, I:K.50, I:T.51, I:R.231 Salt bridges: I:K.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuan, Z. et al., Mechanism of PCNA loading by Ctf18-RFC for leading-strand DNA synthesis. Science (2024)

Release Date

2024-09-04

Peptides

Chromosome transmission fidelity protein 18: A
DNA polymerase epsilon catalytic subunit A: C
Chromosome transmission fidelity protein 8: D
Sister chromatid cohesion protein DCC1: E
Replication factor C subunit 4: F
Replication factor C subunit 3: G
Replication factor C subunit 2: H
Replication factor C subunit 5: I
Chromosome transmission fidelity protein 18: J
Proliferating cell nuclear antigen: KLM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
E

D
D

E
B

F
4

G
3

H
2

I
5

J
1

K
X

L
Y

M
Z

Chromosome transmission fidelity protein 18

DNA polymerase epsilon catalytic subunit A

Chromosome transmission fidelity protein 8

Sister chromatid cohesion protein DCC1

Replication factor C subunit 4

Replication factor C subunit 3

Replication factor C subunit 2

Replication factor C subunit 5

Chromosome transmission fidelity protein 18

Proliferating cell nuclear antigen

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