6S1N

Human polymerase delta holoenzyme Conformer 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.86 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 processive human Pol delta holoenzyme.

Lancey, C.Tehseen, M.Raducanu, V.S.Rashid, F.Merino, N.Ragan, T.J.Savva, C.G.Zaher, M.S.Shirbini, A.Blanco, F.J.Hamdan, S.M.De Biasio, A.

(2020) Nat Commun 11: 1109-1109

  • DOI: https://doi.org/10.1038/s41467-020-14898-6
  • Primary Citation of Related Structures:  
    6S1M, 6S1N, 6S1O, 6TNY, 6TNZ

  • PubMed Abstract: 

    In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. We present the high-resolution cryo-EM structure of the human processive Pol δ-DNA-PCNA complex in the absence and presence of FEN1. Pol δ is anchored to one of the three PCNA monomers through the C-terminal domain of the catalytic subunit. The catalytic core sits on top of PCNA in an open configuration while the regulatory subunits project laterally. This arrangement allows PCNA to thread and stabilize the DNA exiting the catalytic cleft and recruit FEN1 to one unoccupied monomer in a toolbelt fashion. Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. This work sheds light on the structural basis of Pol δ's activity in replicating the human genome.


  • Organizational Affiliation

    Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta catalytic subunit1,107Homo sapiensMutation(s): 0 
Gene Names: POLD1POLD
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P28340 (Homo sapiens)
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Go to UniProtKB:  P28340
GTEx:  ENSG00000062822 
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UniProt GroupP28340
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta subunit 2469Homo sapiensMutation(s): 0 
Gene Names: POLD2
UniProt & NIH Common Fund Data Resources
Find proteins for P49005 (Homo sapiens)
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Go to UniProtKB:  P49005
GTEx:  ENSG00000106628 
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UniProt GroupP49005
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta subunit 3474Homo sapiensMutation(s): 0 
Gene Names: POLD3KIAA0039
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Find proteins for Q15054 (Homo sapiens)
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Go to UniProtKB:  Q15054
GTEx:  ENSG00000077514 
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UniProt GroupQ15054
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta subunit 4137Homo sapiensMutation(s): 0 
Gene Names: POLD4POLDS
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCU8 (Homo sapiens)
Explore Q9HCU8 
Go to UniProtKB:  Q9HCU8
GTEx:  ENSG00000175482 
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UniProt GroupQ9HCU8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferating cell nuclear antigen
E, F, G
264Homo sapiensMutation(s): 0 
Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens)
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Go to UniProtKB:  P12004
GTEx:  ENSG00000132646 
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UniProt GroupP12004
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA primerH [auth P]25synthetic construct
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA templateI [auth T]38synthetic construct
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Data collection, Database references