6KNC

PolD-PCNA-DNA (form B)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Two conformations of DNA polymerase D-PCNA-DNA, an archaeal replisome complex, revealed by cryo-electron microscopy.

Mayanagi, K.Oki, K.Miyazaki, N.Ishino, S.Yamagami, T.Morikawa, K.Iwasaki, K.Kohda, D.Shirai, T.Ishino, Y.

(2020) BMC Biol 18: 152-152

  • DOI: 10.1186/s12915-020-00889-y
  • Primary Citation of Related Structures:  
    6KNB, 6KNC

  • 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 ...

    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).


    Organizational Affiliation

    Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan. ishino@agr.kyushu-u.ac.jp.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase II small subunitA537Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: polBTK1902
EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (PDB Primary Data)
UniProt
Find proteins for Q5JET1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Go to UniProtKB:  Q5JET1
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase D DP2 (DNA polymerase II large) subunitB1324Thermococcus kodakarensisMutation(s): 0 
EC: 2.7.7.7 (UniProt), 3.1.11.1 (UniProt)
UniProt
Find proteins for Q5JET0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
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Go to UniProtKB:  Q5JET0
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase sliding clamp 1C, D, E249Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: pcn1TK0535
UniProt
Find proteins for Q5JF32 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JF32 
Go to UniProtKB:  Q5JF32
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
pri30DNAF30synthetic construct
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsLengthOrganismImage
temp45DNAG30synthetic construct
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18K06089
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan17H01818
Japan Agency for Medical Research and Development (AMED)Japan20am0101069j0004
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18K05442
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan26242075
Japan Science and TechnologyJapanJPMJPR12L9
Japan Agency for Medical Research and Development (AMED)JapanJP19am01010720231

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references