Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 82.92 kDa 
• Atom Count: 5481 
• Residue Count: 616 
• Unique protein chains: 1

2BIV

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

• DOI: 10.2210/pdb2BIV/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-26 Released: 2005-02-08 
• Deposition Author(s): Santiveri, C.M., Allen, M.D., Sait, F., Bycroft, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.229 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

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

• PubMed: 18706910 
• DOI: 10.1016/j.jmb.2008.07.081
• Primary Citation of Related Structures:  
  2VYT, 2BIV


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SEX COMB ON MIDLEG-LIKE PROTEIN 2	A, B, C	243	Homo sapiens	Mutation(s): 0  Gene Names: SCML2
Find proteins for Q9UQR0 (Homo sapiens) Explore Q9UQR0  Go to UniProtKB:  Q9UQR0
NIH Common Fund Data Resources
PHAROS  Q9UQR0 GTEx  ENSG00000102098

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	A, B, C	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
NA	B, 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 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.02	α = 90
b = 88.206	β = 90
c = 186.988	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-26 
• Released Date: 2005-02-08 
Deposition Author(s): Santiveri, C.M., Allen, M.D., Sait, F., Bycroft, M.

Revision History 

• 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