SMTL ID : 8tw7.1

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

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

ADP.1: 15 residues within 4Å: Chain A: 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.17, A:S.17, A:H.18, A:T.47, A:G.48, A:K.49, A:K.50, A:T.51, A:T.51, A:R.231 Salt bridges: A:K.49

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

AGS.2: 21 residues within 4Å: Chain B: V.5, R.9, P.10, D.15, I.16, V.17, G.18, M.43, P.44, G.45, I.46, G.47, K.48, T.49, T.50, N.138, R.167, M.195, R.196, I.199 Ligands: MG.3 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:V.5, B:R.9, B:V.17, B:M.43, B:G.45, B:I.46, B:I.46, B:G.47, B:K.48, B:T.49, B:T.50, C:R.123 Salt bridges: B:K.48 AGS.4: 21 residues within 4Å: Chain C: 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 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:Y.11, C:R.12, C:R.12, C:Y.20, C:G.48, C:T.49, C:T.49, C:T.49, C:G.50, C:K.51, C:T.52, C:S.53, C:S.53, C:R.198 Salt bridges: C:R.12, C:K.51, C:R.198, C:R.198 AGS.6: 20 residues within 4Å: Chain D: 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 Ligands: MG.7 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:Y.18, D:R.19, D:T.27, D:G.55, D:T.56, D:T.56, D:G.57, D:K.58, D:T.59, D:S.60, D:S.60, D:R.216, D:R.216 Salt bridges: D:R.19, D:K.58, D:R.216, D:R.216

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain B: T.49 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.49 MG.5: 3 residues within 4Å: Chain C: T.52, D.109 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.52 MG.7: 3 residues within 4Å: Chain D: T.59, D.127 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.59

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
5

B
4

C
3

D
2

E
1

F
A

G
B

H
C

Replication factor C subunit 5

Replication factor C subunit 4

Replication factor C subunit 3

Replication factor C subunit 2

Chromosome transmission fidelity protein 18

Proliferating cell nuclear antigen

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