5MVL

Crystal structure of an A-DNA dodecamer containing 5-bromouracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.405 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

5-Formylcytosine does not change the global structure of DNA.

Hardwick, J.S.Ptchelkine, D.El-Sagheer, A.H.Tear, I.Singleton, D.Phillips, S.E.V.Lane, A.N.Brown, T.

(2017) Nat. Struct. Mol. Biol. 24: 544-552

  • DOI: 10.1038/nsmb.3411
  • Primary Citation of Related Structures:  5MVK, 5MVP, 5MVQ, 5MVT, 5MVU

  • PubMed Abstract: 
  • The mechanism by which the recently identified DNA modification 5-formylcytosine (fC) is recognized by epigenetic writer and reader proteins is not known. Recently, an unusual DNA structure, F-DNA, has been proposed as the basis for enzyme recognitio ...

    The mechanism by which the recently identified DNA modification 5-formylcytosine (fC) is recognized by epigenetic writer and reader proteins is not known. Recently, an unusual DNA structure, F-DNA, has been proposed as the basis for enzyme recognition of clusters of fC. We used NMR and X-ray crystallography to compare several modified DNA duplexes with unmodified analogs and found that in the crystal state the duplexes all belong to the A family, whereas in solution they are all members of the B family. We found that, contrary to previous findings, fC does not significantly affect the structure of DNA, although there are modest local differences at the modification sites. Hence, global conformation changes are unlikely to account for the recognition of this modified base, and our structural data favor a mechanism that operates at base-pair resolution for the recognition of fC by epigenome-modifying enzymes.


    Organizational Affiliation

    Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
Brominated DNA dodecamerA,B12synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BRU
Query on BRU
A, B
DNA LINKINGC9 H12 Br N2 O8 PDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.405 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 43.517α = 90.00
b = 43.517β = 90.00
c = 60.850γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
SHELXDphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Biotechnology and Biological Sciences Research CouncilBB/J001694/2

Revision History 

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-05-17
    Type: Database references
  • Version 1.2: 2017-05-24
    Type: Database references
  • Version 1.3: 2017-06-14
    Type: Database references
  • Version 1.4: 2017-08-30
    Type: Author supporting evidence