6KNC

PolD-PCNA-DNA (form B)

Summary for 6KNC

• Entry DOI: 10.2210/pdb6knc/pdb
• EMDB information: 0725
• Descriptor: DNA polymerase II small subunit, DNA polymerase D DP2 (DNA polymerase II large) subunit, DNA polymerase sliding clamp 1, ... (7 entities in total)
• Functional Keywords: family d polymerase, pcna, switch hook, replication, replication-dna complex, replication/dna
• Biological source: Thermococcus kodakarensis KOD1; More
• Total number of polymer chains: 7
• Total formula weight: 314767.07

Authors

Mayanagi, K.,Oki, K.,Miyazaki, N.,Ishino, S.,Yamagami, T.,Iwasaki, K.,Kohda, D.,Morikawa, K.,Shirai, T.,Ishino, Y. (deposition date: 2019-08-05, release date: 2020-08-05, Last modification date: 2024-03-27)

Primary citation

Mayanagi, K.,Oki, K.,Miyazaki, N.,Ishino, S.,Yamagami, T.,Morikawa, K.,Iwasaki, K.,Kohda, D.,Shirai, T.,Ishino, Y.
Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.
Bmc Biol., 18:152-152, 2020

PubMed Abstract: DNA polymerase D (PolD) is the representative member of the D family of DNA polymerases. It is an archaea-specific DNA polymerase required for replication and unrelated to other known DNA polymerases. PolD consists of a heterodimer of two subunits, DP1 and DP2, which contain catalytic sites for 3'-5' editing exonuclease and DNA polymerase activities, respectively, with both proteins being mutually required for the full activities of each enzyme. However, the processivity of the replicase holoenzyme has additionally been shown to be enhanced by the clamp molecule proliferating cell nuclear antigen (PCNA), making it crucial to elucidate the interaction between PolD and PCNA on a structural level for a full understanding of its functional relevance. We present here the 3D structure of a PolD-PCNA-DNA complex from Thermococcus kodakarensis using single-particle cryo-electron microscopy (EM).

PubMed: 33115459
DOI: 10.1186/s12915-020-00889-y

Experimental method

ELECTRON MICROSCOPY (9.3 Å)