Crystal structure of L3MBTL2

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.

Guo, Y.Nady, N.Qi, C.Allali-Hassani, A.Zhu, H.Pan, P.Adams-Cioaba, M.A.Amaya, M.F.Dong, A.Vedadi, M.Schapira, M.Read, R.J.Arrowsmith, C.H.Min, J.

(2009) Nucleic Acids Res 37: 2204-2210

  • DOI: https://doi.org/10.1093/nar/gkp086
  • Primary Citation of Related Structures:  
    3CEY, 3F70

  • PubMed Abstract: 

    The MBT repeat has been recently identified as a key domain capable of methyl-lysine histone recognition. Functional work has pointed to a role for MBT domain-containing proteins in transcriptional repression of developmental control genes such as Hox genes. In this study, L3MBTL2, a human homolog of Drosophila Sfmbt critical for Hox gene silencing, is demonstrated to preferentially recognize lower methylation states of several histone-derived peptides through its fourth MBT repeat. High-resolution crystallographic analysis of the four MBT repeats of this protein reveals its unique asymmetric rhomboid architecture, as well as binding mechanism, which preclude the interaction of the first three MBT repeats with methylated peptides. Structural elucidation of an L3MBTL2-H4K20me1 complex and comparison with other MBT-histone peptide complexes also suggests that an absence of distinct surface contours surrounding the methyl-lysine-binding pocket may underlie the lack of sequence specificity observed for members of this protein family.

  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L6, Ontario, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lethal(3)malignant brain tumor-like 2 protein
A, B
474Homo sapiensMutation(s): 0 
Gene Names: L3MBTL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q969R5 (Homo sapiens)
Explore Q969R5 
Go to UniProtKB:  Q969R5
GTEx:  ENSG00000100395 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ969R5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.643α = 90
b = 55.938β = 90
c = 329.09γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance