SMTL ID : 6t8h.1

Cryo-EM structure of the DNA-bound PolD-PCNA processive complex from P. abyssi

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain B: D.360, H.362, D.404, H.560, H.562 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.360, B:D.360, B:H.362, B:D.404, B:H.562

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain B: D.404, N.450, H.497, H.560 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.404, B:D.404, B:H.497, B:H.560 ZN.3: 5 residues within 4Å: Chain C: C.711, C.714, C.723, N.725, C.726 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.711, C:C.714, C:C.723, C:C.726 ZN.4: 4 residues within 4Å: Chain C: C.736, C.739, C.755, C.758 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.736, C:C.739, C:C.755, C:C.758 ZN.5: 5 residues within 4Å: Chain C: C.1128, C.1131, C.1144, P.1145, C.1147 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.1128, C:C.1131, C:C.1144, C:C.1147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Madru, C. et al., Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA. Nat Commun (2020)

Release Date

2020-03-04

Peptides

DNA polymerase sliding clamp: ADE
DNA polymerase II small subunit: B
DP2 subunit of D-family DNA-polymerase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

D
C

E
D

B
A

C
B

DNA polymerase sliding clamp

DNA polymerase II small subunit

DP2 subunit of D-family DNA-polymerase

Related Entries With Identical Sequence