6TNZ

Human polymerase delta-FEN1-PCNA toolbelt


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 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 subunit
A
1107Homo 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)
Go to UniProtKB:  P28340
NIH Common Fund Data Resources
PHAROS  P28340

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase delta subunit 2
B
469Homo sapiensMutation(s): 0 
Gene Names: POLD2
Find proteins for P49005 (Homo sapiens)
Go to UniProtKB:  P49005
NIH Common Fund Data Resources
PHAROS  P49005

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase delta subunit 3
C
474Homo sapiensMutation(s): 0 
Gene Names: POLD3KIAA0039
Find proteins for Q15054 (Homo sapiens)
Go to UniProtKB:  Q15054
NIH Common Fund Data Resources
PHAROS  Q15054

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase delta subunit 4
D
137Homo sapiensMutation(s): 0 
Gene Names: POLD4POLDS
Find proteins for Q9HCU8 (Homo sapiens)
Go to UniProtKB:  Q9HCU8
NIH Common Fund Data Resources

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
E, F, G
264Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to UniProtKB:  P12004
NIH Common Fund Data Resources
PHAROS  P12004

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Flap endonuclease 1
H
380Homo sapiensMutation(s): 0 
Gene Names: FEN1RAD2
EC: 3.1
Find proteins for P39748 (Homo sapiens)
Go to UniProtKB:  P39748
NIH Common Fund Data Resources
PHAROS  P39748

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsLengthOrganism
DNA primerP25synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsLengthOrganism
DNA templateT38synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP

Download CCD File 
A
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
SF4
Query on SF4

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.05 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History 

  • Version 1.0: 2019-12-18
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Data collection, Database references