SMTL ID : 8unf.1

Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-4-1-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain F: E.12, Y.15, R.16, P.17, C.23, I.24, G.53, T.54, G.55, K.56, T.57, T.58, F.204, R.205 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:E.12, F:Y.15, F:I.24, F:G.53, F:T.54, F:G.55, F:G.55, F:K.56, F:T.57, F:T.58, F:T.58 Salt bridges: F:R.16, F:K.56, F:R.205

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain F: T.57, D.107 Ligands: ADP.1 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.57 MG.4: 5 residues within 4Å: Chain F: E.126 Chain G: T.57, D.107, E.108 Ligands: 08T.3 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.57, G:E.108 MG.6: 6 residues within 4Å: Chain G: R.151 Chain H: T.57, D.107, E.108, T.137 Ligands: 08T.5 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:T.57, H:D.107, H:E.108 MG.8: 6 residues within 4Å: Chain H: R.151 Chain I: T.57, D.107, E.108, T.137 Ligands: 08T.7 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.57, I:E.108

3 x 08T: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium(Non-covalent)

08T.3: 22 residues within 4Å: Chain F: E.126, R.151 Chain G: E.12, Y.15, R.16, P.17, C.23, I.24, L.25, P.52, G.53, T.54, G.55, K.56, T.57, T.58, E.108, N.139, F.204, R.205, I.208 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:Y.15, G:R.16, G:I.24, G:G.53, G:T.54, G:T.54, G:G.55, G:K.56, G:T.57, G:T.58, G:T.58, G:T.58 Salt bridges: G:R.16, G:K.56, G:R.205, G:R.205 08T.5: 22 residues within 4Å: Chain G: E.126, R.151 Chain H: E.12, Y.15, R.16, P.17, C.23, I.24, P.52, G.53, T.54, G.55, K.56, T.57, T.58, E.108, N.139, R.175, F.204, R.205, I.208 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain H Hydrogen bonds: H:Y.15, H:R.16, H:I.24, H:G.53, H:T.54, H:G.55, H:K.56, H:T.57, H:T.58, H:T.58, H:T.58 Salt bridges: H:R.16, H:K.56, H:R.205, H:R.205 08T.7: 21 residues within 4Å: Chain H: E.126, R.151 Chain I: E.12, Y.15, R.16, P.17, C.23, I.24, P.52, G.53, T.54, G.55, K.56, T.57, T.58, E.108, N.139, F.204, R.205, I.208 Ligands: MG.8 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:Y.15, I:I.24, I:G.53, I:T.54, I:G.55, I:K.56, I:T.57, I:T.58, I:T.58 Salt bridges: I:R.16, I:K.56, I:R.205, I:R.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marcus, K. et al., Autoinhibition of a clamp-loader ATPase revealed by deep mutagenesis and cryo-EM. Nat.Struct.Mol.Biol. (2024)

Release Date

2023-12-13

Peptides

Sliding clamp: CDE
Sliding-clamp-loader large subunit: FGHI
Sliding-clamp-loader small subunit: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
H

D
G

E
F

F
E

G
D

H
C

I
B

J
A

Sliding clamp

Sliding-clamp-loader large subunit

Sliding-clamp-loader small subunit

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