5NAF

Co-crystal structure of an MeCP2 peptide with TBLR1 WD40 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the MeCP2-TBLR1 complex reveals a molecular basis for Rett syndrome and related disorders.

Kruusvee, V.Lyst, M.J.Taylor, C.Tarnauskaite, Z.Bird, A.P.Cook, A.G.

(2017) Proc Natl Acad Sci U S A 114: E3243-E3250

  • DOI: https://doi.org/10.1073/pnas.1700731114
  • Primary Citation of Related Structures:  
    5NAF

  • PubMed Abstract: 

    Rett syndrome (RTT) is an X-linked neurological disorder caused by mutations in the methyl-CpG-binding protein 2 ( MeCP2 ) gene. The majority of RTT missense mutations disrupt the interaction of the MeCP2 with DNA or the nuclear receptor corepressor (NCoR)/silencing mediator of retinoic acid and thyroid receptors (SMRT) corepressor complex. Here, we show that the "NCoR/SMRT interaction domain" (NID) of MeCP2 directly contacts transducin beta-like 1 (TBL1) and TBL1 related (TBLR1), two paralogs that are core components of NCoR/SMRT. We determine the cocrystal structure of the MeCP2 NID in complex with the WD40 domain of TBLR1 and confirm by in vitro and ex vivo assays that mutation of interacting residues of TBLR1 and TBL1 disrupts binding to MeCP2. Strikingly, the four MeCP2-NID residues mutated in RTT are those residues that make the most extensive contacts with TBLR1. Moreover, missense mutations in the gene for TBLR1 that are associated with intellectual disability also prevent MeCP2 binding. Our study therefore reveals the molecular basis of an interaction that is crucial for optimal brain function.


  • Organizational Affiliation

    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
F-box-like/WD repeat-containing protein TBL1XR1
A, B, C, D
402Mus musculusMutation(s): 0 
Gene Names: Tbl1xr1Ira1Tblr1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8BHJ5 (Mus musculus)
Explore Q8BHJ5 
Go to UniProtKB:  Q8BHJ5
IMPC:  MGI:2441730
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8BHJ5
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Methyl-CpG-binding protein 2
E, F
25Mus musculusMutation(s): 0 
UniProt
Find proteins for Q9Z2D6 (Mus musculus)
Explore Q9Z2D6 
Go to UniProtKB:  Q9Z2D6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z2D6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth C],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
X [auth D],
Y [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.628α = 97.63
b = 58.643β = 91.17
c = 155.101γ = 90.24
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomG1000520/1
Wellcome TrustUnited Kingdom091580
Wellcome TrustUnited Kingdom107930
Wellcome TrustUnited Kingdom092076
Wellcome TrustUnited Kingdom095822
Wellcome TrustUnited Kingdom108504
Rett Syndrome TrustUnited KingdomGrant to APB

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2017-04-26
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Refinement description