Crystal structure of MvNei1/THF complex

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.213 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Structural Characterization of a Viral NEIL1 Ortholog Unliganded and Bound to Abasic Site-containing DNA

Imamura, K.Wallace, S.S.Doublie, S.

(2009) J Biol Chem 284: 26174-26183

  • DOI: https://doi.org/10.1074/jbc.M109.021907
  • Primary Citation of Related Structures:  
    3A42, 3A45, 3A46

  • PubMed Abstract: 

    Endonuclease VIII (Nei) is a DNA glycosylase of the base excision repair pathway that recognizes and excises oxidized pyrimidines. We determined the crystal structures of a NEIL1 ortholog from the giant Mimivirus (MvNei1) unliganded and bound to DNA containing tetrahydrofuran (THF), which is the first structure of any Nei with an abasic site analog. The MvNei1 structures exhibit the same overall architecture as other enzymes of the Fpg/Nei family, which consists of two globular domains joined by a linker region. MvNei1 harbors a zincless finger, first described in human NEIL1, rather than the signature zinc finger generally found in the Fpg/Nei family. In contrast to Escherichia coli Nei, where a dramatic conformational change was observed upon binding DNA, the structure of MvNei1 bound to DNA does not reveal any substantial movement compared with the unliganded enzyme. A protein segment encompassing residues 217-245 in MvNei1 corresponds to the "missing loop" in E. coli Nei and the "alphaF-beta10 loop" in E. coli Fpg, which has been reported to be involved in lesion recognition. Interestingly, the corresponding loop in MvNei1 is ordered in both the unliganded and furan-bound structures, unlike other Fpg/Nei enzymes where the loop is generally ordered in the unliganded enzyme or in complexes with a lesion, and disordered otherwise. In the MvNei1.tetrahydrofuran complex a tyrosine located at the tip of the putative lesion recognition loop stacks against the furan ring; the tyrosine is predicted to adopt a different conformation to accommodate a modified base.

  • Organizational Affiliation

    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont 05405-0068, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formamidopyrimidine-DNA glycosylase
A, B
289Acanthamoeba polyphaga mimivirusMutation(s): 0 
Gene Names: L315MIMI_L315
EC: (PDB Primary Data), (UniProt)
Find proteins for Q5UQ00 (Acanthamoeba polyphaga mimivirus)
Explore Q5UQ00 
Go to UniProtKB:  Q5UQ00
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5UQ00
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
C, E
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
D, F
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.513α = 90
b = 121.462β = 95.5
c = 80.51γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description