9EKB | pdb_00009ekb

Cryo-EM structure of apo-form human DNA polymerase delta

  • Classification: REPLICATION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2024-12-02 Released: 2025-02-05 
  • Deposition Author(s): Murakami, K.S., Shin, Y.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of apo-form human DNA polymerase delta elucidates its minimal DNA synthesis activity without PCNA.

Shin, Y.Hedglin, M.Murakami, K.S.

(2025) J Biological Chem 301: 108342-108342

  • DOI: https://doi.org/10.1016/j.jbc.2025.108342
  • Primary Citation of Related Structures:  
    9EKB

  • PubMed Abstract: 

    DNA polymerase δ (Pol δ) is a key enzyme in eukaryotic DNA replication and genome maintenance, essential for lagging strand synthesis, leading strand initiation, and DNA repair. While human Pol δ exhibits high activity and processivity in its holoenzyme form complexed with proliferating cell nuclear antigen (PCNA), it shows minimal DNA synthesis activity without PCNA, the molecular basis of which remains unclear. Here, we present the cryo-EM structure of the apo-form human Pol δ, comprising the catalytic subunit p125 and regulatory subunits p66, p50, and p12, at an overall resolution of 3.65 Å. We identified an acidic α-helix at the N-terminus of p125, which occupies the single-stranded DNA-binding cavity within the polymerase domain in the apo-form Pol δ. This interaction likely inhibits DNA binding in the absence of PCNA, explaining the low activity of apo-form Pol δ. The acidic α-helix is absent in yeast Pol δ, providing a molecular explanation for species-specific differences in PCNA-independent Pol δ activity. These findings provide critical insights into the regulatory mechanisms of Pol δ and its reliance on PCNA for efficient DNA synthesis.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, The Center for RNA Molecular Biology, The Center for Structural Biology, The Pennsylvania State University, University Park, PA 16802, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P28340 
Go to UniProtKB:  P28340
PHAROS:  P28340
GTEx:  ENSG00000062822 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28340
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore P49005 
Go to UniProtKB:  P49005
PHAROS:  P49005
GTEx:  ENSG00000106628 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49005
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta subunit 3466Homo sapiensMutation(s): 0 
Gene Names: POLD3KIAA0039
UniProt & NIH Common Fund Data Resources
Find proteins for Q15054 (Homo sapiens)
Explore Q15054 
Go to UniProtKB:  Q15054
PHAROS:  Q15054
GTEx:  ENSG00000077514 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15054
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta subunit 4114Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HCU8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIXdev_5330

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM131860
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM147238

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-03-12
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-02
    Changes: Data collection, Database references