6HMS

Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 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

Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases.

Raia, P., Carroni, M., Henry, E., Pehau-Arnaudet, G., Brule, S., Beguin, P., Henneke, G., Lindahl, E., Delarue, M., Sauguet, L.

(2019) PLoS Biol 17: e3000122-e3000122

  • DOI: https://doi.org/10.1371/journal.pbio.3000122
  • Primary Citation of Related Structures:  
    6HMF, 6HMS

  • PubMed Abstract: 

    • PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP) ...

    PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.

    Organizational Affiliation: 

    Unit of Structural Dynamics of Macromolecules, Pasteur Institute and CNRS UMR 3528, Paris, France.



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase II small subunit400Pyrococcus abyssiMutation(s): 0 
Gene Names: polB, PYRAB01210, PAB2266
EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (PDB Primary Data)
UniProt
Find proteins for Q9V2F3 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2F3 
Go to UniProtKB:  Q9V2F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V2F3
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase II large subunit,DNA polymerase II large subunit1,270Pyrococcus abyssiMutation(s): 0 
Gene Names: polC, PYRAB01200, PAB2404
EC: 2.7.7.7 (PDB Primary Data), 3.1.11.1 (PDB Primary Data)
UniProt
Find proteins for Q9V2F4 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2F4 
Go to UniProtKB:  Q9V2F4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V2F4
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*AP*GP*AP*CP*GP*GP*GP*CP*CP*GP*CP*GP*TP*C)-3')C [auth P]15Pyrococcus abyssi
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*GP*AP*CP*GP*CP*GP*GP*CP*CP*CP*GP*TP*CP*TP*C)-3')D [auth T]16Pyrococcus abyssi
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR -17-CE11-0005

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Other