2PQW

Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), trigonal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

L3MBTL1 recognition of mono- and dimethylated histones.

Min, J.Allali-Hassani, A.Nady, N.Qi, C.Ouyang, H.Liu, Y.MacKenzie, F.Vedadi, M.Arrowsmith, C.H.

(2007) Nat.Struct.Mol.Biol. 14: 1229-1230

  • DOI: 10.1038/nsmb1340
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of the L3MBTL1 MBT repeats in complex with histone H4 peptides dimethylated on Lys20 (H4K20me2) show that only the second of the three MBT repeats can bind mono- and dimethylated histone peptides. Its binding pocket has similaritie ...

    Crystal structures of the L3MBTL1 MBT repeats in complex with histone H4 peptides dimethylated on Lys20 (H4K20me2) show that only the second of the three MBT repeats can bind mono- and dimethylated histone peptides. Its binding pocket has similarities to that of 53BP1 and is able to recognize the degree of histone lysine methylation. An unexpected mode of peptide-mediated dimerization suggests a possible mechanism for chromatin compaction by L3MBTL1.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario, M5G 1L5, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lethal(3)malignant brain tumor-like protein
A
323Homo sapiensMutation(s): 0 
Gene Names: L3MBTL1 (KIAA0681, L3MBT, L3MBTL)
Find proteins for Q9Y468 (Homo sapiens)
Go to Gene View: L3MBTL1
Go to UniProtKB:  Q9Y468
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
B
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
B
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 117.013α = 90.00
b = 117.013β = 90.00
c = 90.380γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOLREPphasing
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-07-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance