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 report here the solution structure of the MBD of the human methylation-dependent transcriptional regulator MBD1 bound to methylated DNA ...

    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 ProteinC [auth A]75Homo sapiensMutation(s): 0 
Gene Names: MBD1CXXC3PCM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UIS9 (Homo sapiens)
Explore Q9UIS9 
Go to UniProtKB:  Q9UIS9
PHAROS:  Q9UIS9
Protein Feature View
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  • 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'A [auth B], B [auth C]12N/A
    Protein Feature View
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    • Reference Sequence
    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  (Full details and data files)

    • 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