6S1M

Human polymerase delta holoenzyme Conformer 1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.27 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
  • 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 ...

    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 LengthOrganismDetailsImage
DNA polymerase delta catalytic subunitA1,107Homo sapiensMutation(s): 0 
Gene Names: POLD1, POLD
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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PHAROS:  P28340
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UniProt GroupP28340
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase delta subunit 2B469Homo sapiensMutation(s): 0 
Gene Names: POLD2
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Find proteins for P49005 (Homo sapiens)
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PHAROS:  P49005
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UniProt GroupP49005
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase delta subunit 3C474Homo sapiensMutation(s): 0 
Gene Names: POLD3, KIAA0039
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Find proteins for Q15054 (Homo sapiens)
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PHAROS:  Q15054
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UniProt GroupQ15054
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase delta subunit 4D137Homo sapiensMutation(s): 0 
Gene Names: POLD4, POLDS
UniProt
Find proteins for Q9HCU8 (Homo sapiens)
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UniProt GroupQ9HCU8
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proliferating cell nuclear antigenE, F, G264Homo sapiensMutation(s): 0 
Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens)
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PHAROS:  P12004
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UniProt GroupP12004
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Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA primerH [auth P]25synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA templateI [auth T]38synthetic construct
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP
Download Ideal Coordinates CCD File 
L [auth T]THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N		 Ligand Interaction
SF4
Query on SF4
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K [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
J [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.27 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