3FDE

Mouse UHRF1 SRA domain bound with hemi-methylated CpG DNA, crystal structure in space group C222(1) at 1.4 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.149 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.

Hashimoto, H.Horton, J.R.Zhang, X.Cheng, X.

(2009) Epigenetics 4: 8-14

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytosine methylation in DNA is a major epigenetic signal, and plays a central role in propagating chromatin status during cell division. However the mechanistic links between DNA methylation and histone methylation are poorly understood. A multi-doma ...

    Cytosine methylation in DNA is a major epigenetic signal, and plays a central role in propagating chromatin status during cell division. However the mechanistic links between DNA methylation and histone methylation are poorly understood. A multi-domain protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for DNA CpG maintenance methylation at replication forks, and mouse UHRF1-null cells show enhanced susceptibility to DNA replication arrest and DNA damaging agents. Recent data demonstrated that the SET and RING associated (SRA) domain of UHRF1 binds hemimethylated CpG and flips 5-methylcytosine out of the DNA helix, whereas its tandom tudor domain and PHD domain bind the tail of histone H3 in a highly methylation sensitive manner. We hypothesize that UHRF1 brings the two components (histones and DNA) carrying appropriate markers (on the tails of H3 and hemimethylated CpG sites) ready to be assembled into a nucleosome after replication.


    Related Citations: 
    • The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
      Hashimoto, H.,Horton, J.R.,Zhang, X.,Bostick, M.,Jacobsen, S.E.,Cheng, X.
      (2008) Nature 455: 826


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase UHRF1
A, B
212Mus musculusMutation(s): 0 
Gene Names: Uhrf1 (Np95)
EC: 2.3.2.27
Find proteins for Q8VDF2 (Mus musculus)
Go to UniProtKB:  Q8VDF2
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'D,C12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'E,F12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, E, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D, E, F
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C, D
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.149 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 84.678α = 90.00
b = 103.691β = 90.00
c = 149.838γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance