SMTL ID : 7tfl.1

Atomic model of S. cerevisiae clamp loader RFC bound to DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

AGS.1: 22 residues within 4Å: Chain A: T.299, A.303, P.304, V.310, C.311, P.355, G.356, I.357, G.358, K.359, T.360, T.361, E.425, I.454, N.456, I.514, R.515, I.518 Chain B: R.128, P.153, R.157 Ligands: MG.2 20 PLIP interactions: 18 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.299, A:C.311, A:C.311, A:G.356, A:I.357, A:G.358, A:K.359, A:T.360, A:T.360, A:T.360, A:T.361, A:T.361, A:E.425, A:R.515, A:R.515, B:R.157, B:R.157 Salt bridges: A:K.359, A:R.515, A:R.515 AGS.3: 19 residues within 4Å: Chain B: V.12, Y.15, R.16, P.17, I.23, V.24, P.51, G.52, I.53, G.54, K.55, T.56, T.57, E.115, A.143, M.202, R.203 Chain C: R.160 Ligands: MG.4 14 PLIP interactions: 1 interactions with chain C, 13 interactions with chain B Hydrogen bonds: C:R.160, B:Y.15, B:V.24, B:G.52, B:I.53, B:I.53, B:G.54, B:K.55, B:T.56, B:T.57, B:R.203 Salt bridges: B:K.55, B:R.203, B:R.203 AGS.5: 21 residues within 4Å: Chain C: V.16, Y.19, R.20, P.21, E.26, V.27, Y.28, P.55, G.56, T.57, G.58, K.59, T.60, S.61, L.169, R.177, M.205, R.206 Chain D: E.158, R.183 Ligands: MG.6 19 PLIP interactions: 17 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:Y.19, C:R.20, C:Y.28, C:Y.28, C:G.56, C:T.57, C:G.58, C:K.59, C:K.59, C:T.60, C:S.61, C:R.177, C:R.206, C:R.206, D:R.183, D:R.183 Salt bridges: C:R.20, C:R.206, C:R.206 AGS.7: 22 residues within 4Å: Chain D: W.27, V.28, Y.31, R.32, P.33, V.39, A.41, Q.42, P.67, G.68, T.69, G.70, K.71, T.72, S.73, R.200, L.228, R.229 Chain E: R.155, E.159, R.184 Ligands: MG.8 21 PLIP interactions: 18 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:V.28, D:Y.31, D:G.68, D:T.69, D:T.69, D:T.69, D:G.70, D:K.71, D:T.72, D:T.72, D:S.73, D:S.73, D:R.229, D:R.229, E:E.159, E:R.184, E:R.184 Salt bridges: D:R.32, D:K.71, D:R.229, D:R.229

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.360, D.424, E.425, I.454 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.360 MG.4: 5 residues within 4Å: Chain B: T.56, D.114, E.115 Chain C: R.160 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.115 MG.6: 6 residues within 4Å: Chain C: T.60, D.117 Chain D: R.155, E.158, R.183 Ligands: AGS.5 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain D: T.72 Chain E: R.156, E.159 Ligands: AGS.7 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain D Metal complexes: E:E.159, E:E.159, D:T.72

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

ADP.9: 18 residues within 4Å: Chain E: V.5, Y.8, R.9, P.10, A.15, L.16, S.17, H.18, N.45, G.46, T.47, G.48, K.49, K.50, T.51, R.52, I.201, R.231 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Y.8, E:A.15, E:S.17, E:H.18, E:G.46, E:T.47, E:G.48, E:K.49, E:K.50, E:T.51, E:T.51, E:R.52, E:R.52 Salt bridges: E:K.49, E:R.231, E:R.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, F. et al., Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. Elife (2022)

Release Date

2022-11-16

Peptides

Replication factor C subunit 1: A
Replication factor C subunit 4: B
Replication factor C subunit 3: C
Replication factor C subunit 2: D
Replication factor C subunit 5: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Replication factor C subunit 1

Replication factor C subunit 4

Replication factor C subunit 3

Replication factor C subunit 2

Replication factor C subunit 5

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