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 
  • R-Value Observed: 0.151 

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

  • DOI: 10.4161/epi.4.1.7370
  • Primary Citation of Related Structures:  
    3F8I, 3F8J, 3FDE

  • 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-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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF1A, B212Mus musculusMutation(s): 0 
Gene Names: Np95Uhrf1
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q8VDF2 (Mus musculus)
Explore Q8VDF2 
Go to UniProtKB:  Q8VDF2
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*AP*TP*GP*(5CM)P*GP*CP*TP*GP*AP*C)-3'C [auth D], E [auth C]12N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*TP*CP*AP*GP*CP*GP*CP*AP*TP*GP*G)-3'D [auth E], F12N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      EDO
      Query on EDO

      Download Ideal Coordinates CCD File 
      BA [auth D] , CA [auth E] , DA [auth E] , FA [auth C] , G [auth A] , H [auth A] , I [auth A] , J [auth A] , 
      BA [auth D],  CA [auth E],  DA [auth E],  FA [auth C],  G [auth A],  H [auth A],  I [auth A],  J [auth A],  JA [auth F],  K [auth A],  KA [auth F],  L [auth A],  LA [auth F],  M [auth A],  MA [auth F],  N [auth A],  NA [auth F],  R [auth B],  S [auth B],  T [auth B],  U [auth B],  V [auth B]
      1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N
       Ligand Interaction
      NA
      Query on NA

      Download Ideal Coordinates CCD File 
      EA [auth E], O [auth A], OA [auth F], W [auth B]SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      UNL
      Query on UNL

      Download Ideal Coordinates CCD File 
      AA [auth B] , GA [auth C] , HA [auth C] , IA [auth C] , P [auth A] , Q [auth A] , X [auth B] , Y [auth B] , 
      AA [auth B],  GA [auth C],  HA [auth C],  IA [auth C],  P [auth A],  Q [auth A],  X [auth B],  Y [auth B],  Z [auth B]
      Unknown ligand
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.41 Å
      • R-Value Free: 0.186 
      • R-Value Work: 0.149 
      • R-Value Observed: 0.151 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 84.678α = 90
      b = 103.691β = 90
      c = 149.838γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      PHASERphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

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