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 1.2 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: https://doi.org/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. 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

    Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan. maya@bioreg.kyushu-u.ac.jp.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase II small subunit537Thermococcus 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))
Explore Q5JET1 
Go to UniProtKB:  Q5JET1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JET1
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase D DP2 (DNA polymerase II large) subunit1,324Thermococcus kodakarensisMutation(s): 0 
UniProt
Find proteins for Q5JET0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q5JET0 
Go to UniProtKB:  Q5JET0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JET0
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase sliding clamp 1
C, D, E
249Thermococcus 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5JF32
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  • Reference Sequence
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Entity ID: 4
MoleculeChains LengthOrganismImage
pri30DNA30synthetic construct
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains LengthOrganismImage
temp45DNA30synthetic construct
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Refinement description