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


  • 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: 
    • 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
    • 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


    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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Methyl-CpG Binding Protein
A
75Homo sapiensGene Names: MBD1 (CXXC3, PCM1)
Find proteins for Q9UIS9 (Homo sapiens)
Go to Gene View: MBD1
Go to UniProtKB:  Q9UIS9
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'B,C12N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
B, C
DNA LINKINGC10 H16 N3 O7 PDC
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 or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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