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
• NAKB: 9CG4
• EM Map EMD-45568: EMDB EMDataResource

• 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): Fenglin, L., Anna, P.
• 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

cryo-EM structure of FAN1-PCNA-DNA complex in intermediate state

Fenglin, L., Anna, P.

To be published.

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 
• Modelled 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): Fenglin, L., Anna, P.

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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