1IG4

Solution Structure of the Methyl-CpG-Binding Domain of Human MBD1 in Complex with Methylated DNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA.

Ohki, I.Shimotake, N.Fujita, N.Jee, J.Ikegami, T.Nakao, M.Shirakawa, M.

(2001) Cell 105: 487-497

  • DOI: 10.1016/s0092-8674(01)00324-5
  • Primary Citation of Related Structures:  
    1IG4

  • PubMed Abstract: 
  • In vertebrates, the biological consequences of DNA methylation are often mediated by protein factors containing conserved methyl-CpG binding domains (MBDs). Mutations in the MBD protein MeCP2 cause the neurodevelopmental disease Rett syndrome. We rep ...

    In vertebrates, the biological consequences of DNA methylation are often mediated by protein factors containing conserved methyl-CpG binding domains (MBDs). Mutations in the MBD protein MeCP2 cause the neurodevelopmental disease Rett syndrome. We report here the solution structure of the MBD of the human methylation-dependent transcriptional regulator MBD1 bound to methylated DNA. DNA binding causes a loop in MBD1 to fold into a major and novel DNA binding interface. Recognition of the methyl groups and CG sequence at the methylation site is due to five highly conserved residues that form a hydrophobic patch. The structure indicates how MBD may access nucleosomal DNA without encountering steric interference from core histones, and provides a basis to interpret mutations linked to Rett syndrome in MeCP2.


    Related Citations: 
    • Solution structure of the methyl-CpG-binding domain of the methylation-dependent transcriptional repressor MBD1
      Ohki, I., Shimotake, N., Fujita, N., Nakao, M., Shirakawa, M.
      (1999) EMBO J 18: 6653
    • A component of the transcriptional repressor MeCP1 shares a motif with DNA methyltransferase and HRX proteins
      Cross, S.H., Meehan, R.R., Nan, X., Bird, A.
      (1997) Nat Genet 16: 256

    Organizational Affiliation

    Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0101, Nara, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Methyl-CpG Binding ProteinA75Homo sapiensMutation(s): 0 
Gene Names: MBD1CXXC3PCM1
Find proteins for Q9UIS9 (Homo sapiens)
Explore Q9UIS9 
Go to UniProtKB:  Q9UIS9
NIH Common Fund Data Resources
PHAROS  Q9UIS9
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'B, C12N/A
    Experimental Data & Validation

    Experimental Data

    • Method: SOLUTION NMR
    • Conformers Calculated: 200 
    • Conformers Submitted: 20 
    • Selection Criteria: structures with the lowest energy 
    • OLDERADO: 1IG4 Olderado

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2001-05-30
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance