8S5A | pdb_00008s5a

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

• PDB DOI: https://doi.org/10.2210/pdb8S5A/pdb
• NAKB: 8S5A

• Classification: DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-02-23 Released: 2025-03-05 
• Deposition Author(s): Costanzi, E., Thomsen, M.
• Funding Organization(s): Not funded

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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

Literature

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

Costanzi, E., Thomsen, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.43 kDa 
• Atom Count: 5,620 
• Modelled Residue Count: 632 
• Deposited Residue Count: 697 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fanconi-associated nuclease 1	A	654	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: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*CP*AP*CP*GP*CP*CP*TP*AP*GP*AP*CP*TP*CP*CP*TP*CP*A)-3')	B	19	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*GP*GP*CP*GP*TP*G)-3')	C	8	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*GP*AP*GP*GP*AP*GP*TP*CP*TP*T)-3')	D	16	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	G [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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 = 91.626	α = 90
b = 100.547	β = 90
c = 112.879	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-05 
Deposition Author(s): Costanzi, E., Thomsen, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-03-05
  Type: Initial release