9CG4 | pdb_00009cg4

Cryo-EM structure of FAN1, PCNA and DNA substrate with (CAG)2 extrusion in intermediate state

• PDB DOI: https://doi.org/10.2210/pdb9CG4/pdb
• EM Map EMD-45568: EMDB EMDataResource
• NAKB: 9CG4

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct, Annulohypoxylon urceolatum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-28 Released: 2025-02-19 
• Deposition Author(s): Li, F., Pluciennik, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and molecular basis of PCNA-activated FAN1 nuclease function in DNA repair.

Li, F., Phadte, A.S., Bhatia, M., Barndt, S., Monte Carlo Iii, A.R., Hou, C.D., Yang, R., Strock, S., Pluciennik, A.

(2025) Nat Commun 16: 4411-4411

• PubMed: 40368897 
• DOI: https://doi.org/10.1038/s41467-025-59323-y
• Primary Citation Related Structures: 
  9CG4, 9CHM, 9CL7, 9CMA


• PubMed Abstract: 
  

  FAN1 is a DNA dependent nuclease whose proper function is essential for maintaining human health. For example, a genetic variant in FAN1, Arg507 to His hastens onset of Huntington's disease, a repeat expansion disorder for which there is no cure. How the Arg507His mutation affects FAN1 structure and enzymatic function is unknown. Using cryo-EM and biochemistry, we have discovered that FAN1 arginine 507 is critical for its interaction with PCNA, and mutation of Arg507 to His attenuates assembly of the FAN1-PCNA complex on a disease-relevant extrahelical DNA extrusions formed within DNA repeats. This mutation concomitantly abolishes PCNA-FAN1-dependent cleavage of such extrusions, thus unraveling the molecular basis for a specific mutation in FAN1 that dramatically hastens the onset of Huntington's disease. These results underscore the importance of PCNA to the genome stabilizing function of FAN1.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA.
Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
Institution for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, USA.
Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A3B1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 120.44 kDa 
• Atom Count: 8,375 
• Modeled Residue Count: 1,009 
• Deposited Residue Count: 1,009 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proliferating cell nuclear antigen	A [auth B], B [auth C], C [auth D]	261	Homo sapiens	Mutation(s): 0  Gene Names: PCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P12004 (Homo sapiens) Explore P12004  Go to UniProtKB:  P12004
PHAROS:  P12004 GTEx:  ENSG00000132646

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fanconi-associated nuclease 1	D [auth E]	183	Homo sapiens	Mutation(s): 0  Gene Names: FAN1, KIAA1018, MTMR15 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 ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*AP*AP*TP*TP*TP*CP*TP*AP*GP*AP*CP*TP*CP*GP*AP*GP*AP*TP*CP*AP*G)-3')	E [auth A]	23	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*CP*TP*CP*GP*AP*GP*TP*CP*TP*AP*GP*AP*AP*AP*TP*TP*CP*G)-3')	F	20	Annulohypoxylon urceolatum

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.37 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Li, F., Pluciennik, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release
  
• Version 1.1: 2025-09-03
  Changes: Data collection, Database references, Structure summary