2BIV

Crystal structure of the wild-type MBT domains of Human SCML2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

The Malignant Brain Tumor Repeats of Human Scml2 Bind to Peptides Containing Monomethylated Lysine.

Santiveri, C.M., Lechtenberg, B.C., Allen, M.D., Sathyamurthy, A., Jaulent, A.M., Freund, S.M.V., Bycroft, M.

(2008) J.Mol.Biol. 382: 1107

  • DOI: 10.1016/j.jmb.2008.07.081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • SCML2 (sex comb on midleg-like 2) is a constituent of the Polycomb repressive complex 1, a large multiprotein assembly required for the repression of developmental control genes. It contains two MBT (malignant brain tumor) repeats; the MBT is a prote ...

    SCML2 (sex comb on midleg-like 2) is a constituent of the Polycomb repressive complex 1, a large multiprotein assembly required for the repression of developmental control genes. It contains two MBT (malignant brain tumor) repeats; the MBT is a protein module structurally similar to domains that bind to methylated histones. We have used NMR spectroscopy to examine the binding specificity of these repeats. Our data show that they preferentially bind histone peptides monomethylated at lysine residues with no apparent sequence specificity. The crystal structure of the complex between the protein and monomethyllysine reveals that the modified amino acid binds to an aromatic rich pocket at one end of the beta-barrel of the second repeat.

    Organizational Affiliation: 

    MRC Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SEX COMB ON MIDLEG-LIKE PROTEIN 2
A, B, C
243Homo sapiensMutation(s): 0 
Gene Names: SCML2
Find proteins for Q9UQR0 (Homo sapiens)
Go to Gene View: SCML2
Go to UniProtKB:  Q9UQR0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download SDF File 
Download CCD File 
B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD
Download SDF File 
Download CCD File 
A, B, C
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.020α = 90.00
b = 88.206β = 90.00
c = 186.988γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
CNSrefinement
MOSFLMdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy