SMTL ID : 8umv.1

Atomic model of the human CTF18-RFC-PCNA-DNA ternary complex with narrow PCNA opening state I (state 5)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: T.381, D.435 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.381 MG.3: 4 residues within 4Å: Chain B: T.83, D.141 Chain C: R.168 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.83 MG.5: 6 residues within 4Å: Chain C: T.67, D.125, R.214 Chain D: E.168, R.193 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.67 MG.7: 5 residues within 4Å: Chain D: T.85, D.150 Chain E: E.153, R.178 Ligands: AGS.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.85

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

AGS.2: 23 residues within 4Å: Chain A: V.283, F.286, A.287, P.288, E.293, L.295, P.376, G.377, L.378, G.379, K.380, T.381, T.382, N.491, R.521, I.549, R.550, I.553 Chain B: R.155, E.159, P.180, R.184 Ligands: MG.1 18 PLIP interactions: 15 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.377, A:L.378, A:G.379, A:K.380, A:K.380, A:T.381, A:T.382, A:N.491, A:N.491, A:R.521, A:R.550, A:R.550, B:R.155, B:R.184, B:R.184 Salt bridges: A:K.380, A:R.550, A:R.550 AGS.4: 22 residues within 4Å: Chain B: V.39, Y.42, R.43, P.44, I.50, V.51, P.78, G.79, T.80, G.81, K.82, T.83, T.84, N.172, M.229, R.230, L.233 Chain C: R.139, E.143, A.164, R.168 Ligands: MG.3 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:Y.42, B:R.43, B:V.51, B:G.79, B:T.80, B:T.80, B:G.81, B:K.82, B:K.82, B:T.83, B:T.84, B:T.84, B:N.172, B:R.230, C:R.139, C:R.168 Salt bridges: B:R.43, B:K.82, B:R.230, B:R.230 AGS.6: 22 residues within 4Å: Chain C: V.23, Y.26, R.27, P.28, L.34, I.35, P.62, G.63, T.64, G.65, K.66, T.67, S.68, N.156, M.213, R.214, L.217 Chain D: R.164, E.168, P.189, R.193 Ligands: MG.5 22 PLIP interactions: 2 interactions with chain D, 20 interactions with chain C Hydrogen bonds: D:R.164, D:R.193, C:Y.26, C:R.27, C:I.35, C:G.63, C:T.64, C:T.64, C:T.64, C:G.65, C:K.66, C:K.66, C:T.67, C:S.68, C:S.68, C:N.156, C:N.156, C:R.214 Salt bridges: C:R.27, C:K.66, C:R.214, C:R.214 AGS.8: 24 residues within 4Å: Chain D: V.41, Y.44, R.45, P.46, E.51, V.52, A.53, P.80, G.81, T.82, G.83, K.84, T.85, S.86, N.181, R.210, L.238, R.239, I.242 Chain E: R.149, E.153, P.174, R.178 Ligands: MG.7 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:V.41, D:R.45, D:A.53, D:G.81, D:T.82, D:T.82, D:T.82, D:G.83, D:K.84, D:K.84, D:T.85, D:S.86, D:S.86, D:N.181, D:N.181, E:R.149, E:R.178 Salt bridges: D:R.45, D:K.84, D:R.239, D:R.239

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

ADP.9: 18 residues within 4Å: Chain A: R.751 Chain E: V.5, R.9, P.10, L.16, D.17, Y.18, P.43, G.45, A.46, G.47, K.48, K.49, T.50, R.51, V.195, L.223, R.224 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:V.5, E:D.17, E:P.43, E:G.45, E:A.46, E:G.47, E:K.48, E:K.49, E:T.50, E:T.50, E:R.51, E:R.51 Salt bridges: E:K.48, E:R.224, E:R.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, Q. et al., Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC. Proc.Natl.Acad.Sci.USA (2024)

Release Date

2024-05-08

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Chromosome transmission fidelity protein 18 homolog

Replication factor C subunit 2

Replication factor C subunit 5

Replication factor C subunit 4

Replication factor C subunit 3

Proliferating cell nuclear antigen

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