SMTL ID : 8uii.1

Cryo-EM map of human clamp-clamp loader ATAD5-RFC-closed PCNA complex in intermediate state 1

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.1139, E.1305 Ligands: AGS.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.1139, A:E.1305 MG.3: 4 residues within 4Å: Chain B: T.83, R.230 Chain C: R.139 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.83 MG.5: 3 residues within 4Å: Chain C: T.67, D.125 Ligands: AGS.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.67 MG.7: 2 residues within 4Å: Chain D: T.85 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: 22 residues within 4Å: Chain A: T.1055, Q.1059, P.1060, L.1066, I.1067, T.1134, G.1135, V.1136, G.1137, K.1138, T.1139, A.1140, E.1305, E.1306, S.1337, Y.1365, I.1393, R.1394 Chain B: R.155, E.159, R.184 Ligands: MG.1 20 PLIP interactions: 17 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.1055, A:Q.1059, A:I.1067, A:G.1135, A:V.1136, A:V.1136, A:G.1137, A:K.1138, A:T.1139, A:T.1139, A:A.1140, A:Y.1365, A:R.1394, A:R.1394, B:R.155, B:R.184, B:R.184 Salt bridges: A:K.1138, A:R.1394, A:R.1394 AGS.4: 22 residues within 4Å: Chain B: V.39, Y.42, R.43, P.44, E.49, I.50, V.51, P.78, G.79, T.80, G.81, K.82, T.83, T.84, N.172, L.193, M.229, R.230, L.233 Chain C: R.139, A.164 Ligands: MG.3 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.42, B:R.43, 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.83, B:T.84, B:T.84, B:N.172, B:R.230, C:R.139 Salt bridges: B:R.43, B:K.82, B:R.230, B:R.230 AGS.6: 20 residues within 4Å: Chain C: V.23, Y.26, 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 Ligands: MG.5 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:Y.26, C:R.27, C:I.35, C:G.63, 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 Salt bridges: C:R.27, C:K.66, C:R.214, C:R.214 AGS.8: 19 residues within 4Å: Chain D: V.41, Y.44, R.45, P.46, V.52, A.53, P.80, G.81, T.82, G.83, K.84, T.85, S.86, L.202, R.210, L.238, R.239, I.242 Ligands: MG.7 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:V.41, 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: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.9: 20 residues within 4Å: Chain A: N.1789 Chain E: W.4, V.5, R.9, P.10, L.16, D.17, Y.18, S.44, G.45, A.46, G.47, K.48, K.49, T.50, R.51, V.195, L.223, R.224, L.227 18 PLIP interactions: 18 interactions with chain E Hydrogen bonds: E:V.5, E:R.9, E:D.17, E:D.17, E:Y.18, 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:R.9, E:K.48, E:R.224, E:R.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader. Nat.Struct.Mol.Biol. (2024)

Release Date

2024-05-29

Peptides

ATPase family AAA domain-containing protein 5: 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

ATPase family AAA domain-containing protein 5

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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