8S5A | pdb_00008s5a

The crystal structure of FAN1 Nuclease bound to 5' phosphorylated p(dG)/3'(dT-dT-dT-dT) double flap DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 
    0.273 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.236 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A FAN1 point mutation associated with accelerated Huntington's disease progression alters its PCNA-mediated assembly on DNA.

Aretz, J.Jeyasankar, G.Salerno-Kochan, A.Thomsen, M.Thieulin-Pardo, G.Haque, T.Monteagudo, E.Felsenfeld, D.Finley, M.Vogt, T.F.Boudet, J.Prasad, B.C.

(2025) Nat Commun 16: 4412-4412

  • DOI: https://doi.org/10.1038/s41467-025-59324-x
  • Primary Citation of Related Structures:  
    8S5A, 9EO1, 9EOA, 9GY0

  • PubMed Abstract: 

    FAN1 is an endo- and exo-nuclease involved in DNA and interstrand crosslink repair. Genome-wide association studies of people with Huntington's disease revealed a strong association between the FAN1 R507H mutation and early disease onset, however the underlying mechanism(s) remains unclear. FAN1 has previously been implicated in modulating triplet repeat expansion in a PCNA dependent manner. To examine the role of PCNA on FAN1 activation, we solved the cryo-EM structures of a PCNA-FAN1-DNA complex. Our findings reveal that the FAN1 R507 residue directly interacts with PCNA D232. Biophysical interaction studies demonstrated that FAN1 enhances the binding affinity of PCNA for DNA, a synergistic effect disrupted in mutants carrying the R507H mutation. In contrast, PCNA does not affect the affinity of FAN1 for DNA but does modulate FAN1 activity upon ternary complex formation. The weakened and functionally altered FAN1 R507H-PCNA-DNA complex may partly impair the FAN1-mediated repair of CAG extrahelical extrusions, providing a potential explanation for the mutation's role in accelerating disease progression.


  • Organizational Affiliation

    Proteros biostructures GmbH, Bunsenstr. 7a, D - 82152, Martinsried, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fanconi-associated nuclease 1654Homo sapiensMutation(s): 0 
Gene Names: FAN1KIAA1018MTMR15
EC: 3.1.21 (PDB Primary Data), 3.1.4.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2M0 (Homo sapiens)
Explore Q9Y2M0 
Go to UniProtKB:  Q9Y2M0
PHAROS:  Q9Y2M0
GTEx:  ENSG00000198690 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2M0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')19synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3')8synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*T)-3')16synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free:  0.273 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.236 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.626α = 90
b = 100.547β = 90
c = 112.879γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Database references
  • Version 1.2: 2025-07-09
    Changes: Structure summary