SMTL ID : 8umt.1

Atomic model of the human CTF18-RFC-PCNA binary complex in the three-subunit binding state (state 2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain B: T.83, D.141 Ligands: AGS.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.83 MG.3: 3 residues within 4Å: Chain C: T.67, D.125 Ligands: AGS.4 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.67, C:D.125 MG.5: 3 residues within 4Å: Chain D: T.85, D.150 Ligands: AGS.6 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.150, D:D.150

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

AGS.2: 18 residues within 4Å: Chain B: V.39, R.43, P.44, I.50, V.51, G.52, G.79, T.80, G.81, K.82, T.83, T.84, D.141, R.201, M.229, R.230 Chain C: R.139 Ligands: MG.1 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:V.51, B:G.52, B:G.79, B:T.80, B:G.81, B:K.82, B:T.83, B:T.83, B:T.84, B:R.230 Salt bridges: B:K.82 AGS.4: 20 residues within 4Å: Chain C: V.23, R.27, P.28, D.33, L.34, I.35, P.62, G.63, T.64, G.65, K.66, T.67, S.68, N.156, R.185, M.213, R.214, L.217 Chain D: R.165 Ligands: MG.3 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:V.23, C:R.27, C:I.35, C:I.35, C:G.63, C:T.64, C:G.65, C:K.66, C:T.67, C:S.68, C:R.185, D:R.165 Salt bridges: C:R.27, C:K.66, C:R.214 AGS.6: 18 residues within 4Å: Chain D: V.41, Y.44, R.45, P.46, V.52, A.53, Q.55, P.80, G.81, T.82, G.83, K.84, T.85, S.86, R.210, L.238, R.239 Ligands: MG.5 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:V.41, D:Y.44, D:A.53, D:A.53, D:Q.55, D:G.81, D:T.82, D:G.83, D:K.84, D:T.85, D:T.85, D:T.85, D:S.86, D:R.210, D:R.210, D:R.239 Salt bridges: D:R.45, D:K.84

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

ADP.7: 18 residues within 4Å: Chain A: R.751 Chain E: V.5, P.10, L.16, D.17, Y.18, P.43, S.44, G.45, A.46, G.47, K.48, K.49, T.50, R.51, V.195, L.223, R.224 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:V.5, E:D.17, E:D.17, E:G.45, E:A.46, E:G.47, E:K.48, E:K.49, E:T.50, 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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