SMTL ID : 8tw8.1

Cryo-EM structure of S. cerevisiae Ctf18-RFC-PCNA complex in Apo state conformation I

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

AGS.1: 23 residues within 4Å: Chain A: 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 B: E.127, R.152 Ligands: MG.2 18 PLIP interactions: 1 interactions with chain B, 17 interactions with chain A Hydrogen bonds: B:R.152, A:V.9, A:R.13, A:R.13, A:V.21, A:M.47, A:G.49, A:I.50, A:I.50, A:G.51, A:K.52, A:T.53, A:T.54, A:R.200, A:R.200 Salt bridges: A:K.52, A:R.200, A:R.200 AGS.3: 22 residues within 4Å: Chain B: 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 C: R.170 Ligands: MG.4 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.11, B:R.12, B:R.12, B:Y.20, B:G.48, B:T.49, B:T.49, B:T.49, B:T.49, B:G.50, B:K.51, B:T.52, B:T.52, B:S.53, B:S.53, B:R.198, C:R.170, C:R.170 Salt bridges: B:R.12, B:K.51, B:R.198, B:R.198 AGS.5: 23 residues within 4Å: Chain C: 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 D: E.159, P.180, R.184 Ligands: MG.6 20 PLIP interactions: 2 interactions with chain D, 18 interactions with chain C Hydrogen bonds: D:R.184, D:R.184, C:Y.18, C:R.19, C:T.27, C:G.55, C:T.56, C:T.56, C:T.56, C:G.57, C:K.58, C:T.59, C:S.60, C:S.60, C:R.216, C:R.216 Salt bridges: C:R.19, C:K.58, C:R.216, C:R.216

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.53 Chain B: E.127 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.53 MG.4: 4 residues within 4Å: Chain B: T.52, D.109 Chain C: R.170 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.52 MG.6: 5 residues within 4Å: Chain C: T.59, D.127, E.128 Chain D: R.184 Ligands: AGS.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.59

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

ADP.7: 15 residues within 4Å: Chain D: 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 E: F.156 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.17, D:S.17, D:T.47, D:G.48, D:K.49, D:K.50, D:T.51, D:R.231 Salt bridges: D: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

Replication factor C subunit 4: A
Replication factor C subunit 3: B
Replication factor C subunit 2: C
Replication factor C subunit 5: D
Chromosome transmission fidelity protein 18: E
Proliferating cell nuclear antigen: FGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
4

B
3

C
2

D
5

E
1

F
A

G
B

H
C

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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