7Z5A | pdb_00007z5a

Crystal structure of the trapped complex of mouse Endonuclease VIII-LIKE 3 (mNEIL3) and hairpin DNA with 5'overhang

• PDB DOI: https://doi.org/10.2210/pdb7Z5A/pdb
• NAKB: 7Z5A

• Classification: DNA BINDING PROTEIN
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli, synthetic construct
• Mutation(s): No 


• Deposited: 2022-03-08 Released: 2022-10-19 
• Deposition Author(s): Silhan, J., Huskova, A.
• Funding Organization(s): Czech Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Starting Model: experimental

Literature

Model of abasic site DNA cross-link repair; from the architecture of NEIL3 DNA binding domains to the X-structure model.

Huskova, A., Dinesh, D.C., Srb, P., Boura, E., Veverka, V., Silhan, J.

(2022) Nucleic Acids Res 50: 10436-10448

• PubMed: 36155818 
• DOI: https://doi.org/10.1093/nar/gkac793
• Primary Citation Related Structures: 
  7OMK, 7Z5A


• PubMed Abstract: 
  

  Covalent DNA interstrand crosslinks are toxic DNA damage lesions that block the replication machinery that can cause a genomic instability. Ubiquitous abasic DNA sites are particularly susceptible to spontaneous cross-linking with a base from the opposite DNA strand. Detection of a crosslink induces the DNA helicase ubiquitination that recruits NEIL3, a DNA glycosylase responsible for the lesion removal. NEIL3 utilizes several zinc finger domains indispensable for its catalytic NEI domain repairing activity. They recruit NEIL3 to the repair site and bind the single-stranded DNA. However, the molecular mechanism underlying their roles in the repair process is unknown. Here, we report the structure of the tandem zinc-finger GRF domain of NEIL3 and reveal the molecular details of its interaction with DNA. Our biochemical data indicate the preferential binding of the GRF domain to the replication fork. In addition, we obtained a structure for the catalytic NEI domain in complex with the DNA reaction intermediate that allowed us to construct and validate a model for the interplay between the NEI and GRF domains in the recognition of an interstrand cross-link. Our results suggest a mechanism for recognition of the DNA replication X-structure by NEIL3, a key step in the interstrand cross-link repair.

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Organizational Affiliation: 
• Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo namesti 2, 166 10 Prague, Czech Republic.
Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking, gel filtration

Macromolecule Content 

• Total Structure Weight: 39.36 kDa 
• Atom Count: 2,484 
• Modeled Residue Count: 280 
• Deposited Residue Count: 322 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease 8-like 3	A	303	Mus musculus	Mutation(s): 0  Gene Names: Neil3 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for Q8K203 (Mus musculus) Explore Q8K203  Go to UniProtKB:  Q8K203

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*(PED)P*AP*CP*GP*CP*GP*AP*AP*GP*CP*GP*TP*G)-3')	B [auth E]	19	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.248 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.117	α = 90
b = 71.528	β = 90
c = 94.437	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Silhan, J., Huskova, A.

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Funding Organization	Location	Grant Number
Czech Academy of Sciences	Czech Republic	RVO: 61388963

Revision History  

• Version 1.0: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2022-10-26
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary