9DP3

APE1 N174D Product Complex with Abasic DNA

• PDB DOI: https://doi.org/10.2210/pdb9DP3/pdb
• NAKB: 9DP3

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-09-20 Released: 2024-10-09 
• Deposition Author(s): Hoitsma, N.M., DeHart, K.D., Freudenthal, B.D.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.274 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 

Starting Model: experimental

Literature

N174 Physically and Chemically Stabilizes Abasic DNA During the APE1 Endonuclease Reaction

DeHart, K.D., Hoitsma, N.M., Thompson, S.H., Freudenthal, B.D.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.15 kDa 
• Atom Count: 5,445 
• Modelled Residue Count: 584 
• Deposited Residue Count: 594 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair nuclease/redox regulator APEX1, mitochondrial	A, B	276	Homo sapiens	Mutation(s): 2  Gene Names: APEX1, APE, APE1, APEX, APX, HAP1, REF1 EC: 3.1.21 (UniProt), 3.1.11.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P27695 (Homo sapiens) Explore P27695  Go to UniProtKB:  P27695
PHAROS:  P27695 GTEx:  ENSG00000100823

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')	C [auth D]	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')	D [auth E]	10	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	E [auth F]	21	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.274 
• R-Value Work: 0.253 
• R-Value Observed: 0.255 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.205	α = 82.55
b = 60.834	β = 77.17
c = 73.619	γ = 85.85

Software Package:

Software Name	Purpose
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-09 
Deposition Author(s): Hoitsma, N.M., DeHart, K.D., Freudenthal, B.D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	R01 ES029203

Revision History  

• Version 1.0: 2024-10-09
  Type: Initial release