9RQS | pdb_00009rqs

Human APE1 in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb9RQS/pdb
• NAKB: 9RQS

• Classification: HYDROLASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-06-26 Released: 2026-05-13 
• Deposition Author(s): Ludaescher, J.M., Scaletti Hutchinson, E., Stenmark, P.
• Funding Organization(s): Cancerfonden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.228 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.198 (DCC) 

Starting Model: experimental

Literature

Structural basis for uracil removal from DNA by human SMUG1.

Ludascher, J.M., Scaletti Hutchinson, E., Vila-Julia, G., Jemth, A.S., Shahid, S., Wiita, E., Cabeza de Vaca, I., Pach, S., Gajdos, L., Aggarwal, S., Walse, E., Mortusewicz, O., Helleday, T., Carlsson, J., Stenmark, P.

(2026) Nat Commun 17

• PubMed: 42230560 
• DOI: https://doi.org/10.1038/s41467-026-72937-0
• Primary Citation Related Structures: 
  9GGS, 9GK0, 9GM2, 9RQP, 9RQS


• PubMed Abstract: 
  

  Human single-strand-selective monofunctional uracil DNA glycosylase 1 (hSMUG1) removes uracil, 5-hydroxymethyluracil (5hmU) and 5-fluorouracil (5FU) from DNA, thereby initiating the base excision repair (BER) process. hSMUG1 is important for maintaining genomic integrity and plays a significant role in cancer biology. Here, we present the structures of hSMUG1, including complexes with products (uracil and 5FU) and an enzyme-product complex of hSMUG1 with double-stranded DNA (dsDNA). Analysis of our hSMUG1-dsDNA complex reveals how uracil is flipped out of the dsDNA for excision and identifies key residues that we confirm to be critical for both DNA binding and enzymatic activity. Furthermore, our hSMUG1 substrate complexes, molecular dynamics simulations and neutron diffraction data suggest a mechanism by which the substrate uracil rotates following base excision. The structural and functional information presented here will be highly useful for the future development of inhibitors and/or activators targeting hSMUG1.

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Organizational Affiliation: 
• Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden.
Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden.
Large Scale Structures group, Institut Laue-Langevin (ILL), Grenoble, France.
European Spallation Source (ESS), Lund, Sweden.
Division of Computational Chemistry, Lund University, Lund, Sweden.
Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 38.8 kDa 
• Atom Count: 2,802 
• Modeled Residue Count: 292 
• Deposited Residue Count: 304 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair nuclease/redox regulator APEX1, mitochondrial	A	280	Homo sapiens	Mutation(s): 0  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*CP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*G)-3')	B [auth D]	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*GP*GP*AP*CP*T*(LIG)P*(AS)P*CP*GP*GP*G)-3')	C [auth E]	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.228 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.198 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.122	α = 90
b = 71.707	β = 110.571
c = 75.274	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-13 
Deposition Author(s): Ludaescher, J.M., Scaletti Hutchinson, E., Stenmark, P.

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Funding Organization	Location	Grant Number
Cancerfonden	Sweden	--

Revision History  

• Version 1.0: 2026-05-13
  Type: Initial release
  
• Version 1.1: 2026-06-17
  Changes: Database references