6S1O

Human polymerase delta holoenzyme Conformer 3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 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 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: 10.1038/s41467-020-14898-6
  • Structures With Same Primary Citation

  • 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-resol ...

    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

    Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester, LE1 7HB, UK. adb43@leicester.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase delta catalytic subunitA1107Homo sapiensMutation(s): 0 
Gene Names: POLD1POLD
EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (PDB Primary Data)
Find proteins for P28340 (Homo sapiens)
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Go to UniProtKB:  P28340
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PHAROS  P28340
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase delta subunit 2B469Homo sapiensMutation(s): 0 
Gene Names: POLD2
Find proteins for P49005 (Homo sapiens)
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PHAROS  P49005
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase delta subunit 3C474Homo sapiensMutation(s): 0 
Gene Names: POLD3KIAA0039
Find proteins for Q15054 (Homo sapiens)
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PHAROS  Q15054
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase delta subunit 4D137Homo sapiensMutation(s): 0 
Gene Names: POLD4POLDS
Find proteins for Q9HCU8 (Homo sapiens)
Explore Q9HCU8 
Go to UniProtKB:  Q9HCU8
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigenE, F, G264Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Explore P12004 
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PHAROS  P12004
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  • Reference Sequence

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Entity ID: 7
MoleculeChainsLengthOrganism
DNA templateT38synthetic construct

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Entity ID: 6
MoleculeChainsLengthOrganism
DNA primerP25synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP

Download CCD File 
T
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
SF4
Query on SF4

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A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.10 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 

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