2BIV | pdb_00002biv

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.229 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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 Biology 382: 1107

  • DOI: https://doi.org/10.1016/j.jmb.2008.07.081
  • Primary Citation of Related Structures:  
    2BIV, 2VYT

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SEX COMB ON MIDLEG-LIKE PROTEIN 2
A, B, C
243Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQR0 (Homo sapiens)
Explore Q9UQR0 
Go to UniProtKB:  Q9UQR0
PHAROS:  Q9UQR0
GTEx:  ENSG00000102098 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQR0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD
Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth B]
H [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth B],
H [auth B],
J [auth B],
K [auth C],
L [auth C],
M [auth C],
O [auth C]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
NA
Query on NA
Download Ideal Coordinates CCD File 
I [auth B],
N [auth C]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.229 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.02α = 90
b = 88.206β = 90
c = 186.988γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2014-02-05
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description