6YWW

MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion.

Ibrahim, A.Papin, C.Mohideen-Abdul, K.Le Gras, S.Stoll, I.Bronner, C.Dimitrov, S.Klaholz, B.P.Hamiche, A.

(2021) Science 372

  • DOI: https://doi.org/10.1126/science.abd5581
  • Primary Citation of Related Structures:  
    6YWW

  • PubMed Abstract: 

    The Rett syndrome protein MeCP2 was described as a methyl-CpG-binding protein, but its exact function remains unknown. Here we show that mouse MeCP2 is a microsatellite binding protein that specifically recognizes hydroxymethylated CA repeats. Depletion of MeCP2 alters chromatin organization of CA repeats and lamina-associated domains and results in nucleosome accumulation on CA repeats and genome-wide transcriptional dysregulation. The structure of MeCP2 in complex with a hydroxymethylated CA repeat reveals a characteristic DNA shape, with considerably modified geometry at the 5-hydroxymethylcytosine, which is recognized specifically by Arg 133 , a key residue whose mutation causes Rett syndrome. Our work identifies MeCP2 as a microsatellite DNA binding protein that targets the 5hmC-modified CA-rich strand and maintains genome regions nucleosome-free, suggesting a role for MeCP2 dysfunction in Rett syndrome.


  • Organizational Affiliation

    Institute of Genetics and of Molecular and Cellular Biology (IGBMC), 67400 Illkirch, France.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Truncated methyl CpG binding protein 2 transcript 1101Homo sapiensMutation(s): 0 
Gene Names: MECP2
UniProt & NIH Common Fund Data Resources
Find proteins for P51608 (Homo sapiens)
Explore P51608 
Go to UniProtKB:  P51608
PHAROS:  P51608
GTEx:  ENSG00000169057 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51608
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA/RNA (5'-D(*TP*CP*TP*GP*CP*AP*CP*A)-R(P*(5HC))-D(P*AP*CP*AP*CP*AP*AP*TP*TP*AP*TP*A)-3')20synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*AP*TP*AP*AP*TP*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*CP*AP*G)-3')20synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.377α = 90
b = 48.986β = 90.53
c = 66.187γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references, Structure summary
  • Version 1.2: 2021-07-28
    Changes: Structure summary
  • Version 1.3: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.4: 2024-01-24
    Changes: Data collection, Refinement description