1OI1 | pdb_00001oi1

Crystal Structure of the MBT domains of Human SCML2

• PDB DOI: https://doi.org/10.2210/pdb1OI1/pdb

• Classification: MBT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-06-04 Released: 2003-06-15 
• Deposition Author(s): Sathyamurthy, A., Allen, M.D., Murzin, A.G., Bycroft, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.204 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Literature

Crystal Structure of the Malignant Brain Tumor (Mbt) Repeats in Sex Comb on Midleg-Like 2 (Scml2).

Sathyamurthy, A., Allen, M.D., Murzin, A.G., Bycroft, M.

(2003) J Biological Chem 278: 46968

• PubMed: 12952983 
• DOI: https://doi.org/10.1074/jbc.M306469200
• Primary Citation of Related Structures:  
  1OI1


• PubMed Abstract: 
  

  Sex Comb on Midleg (SCM) belongs to the Polycomb group of proteins, which are involved in transcriptional regulation in Drosophila. It is one of the components of Polycomb repressive complex 1, a multiprotein complex of Polycomb group proteins involved in the maintenance of repression and the blocking of chromatin remodeling. SCM contains two approximately 100-residue malignant brain tumor (MBT) repeats at the N terminus. These repeats are also found in other proteins involved in transcriptional repression. Here, we report the 1.78-A crystal structure of the two MBT repeats of SCM-like 2 (SCML2), a human homologue of SCM. Each repeat consists of an extended arm and a beta-barrel core. There are significant structural similarities to the Tudor, PWWP, and chromo domains, suggesting probable evolutionary relationships and functional similarities between the MBT repeats and these domains.

---

Organizational Affiliation: 

Medical Research Council Centre for Protein Engineering, Hills Road, Cambridge CB2 2QH, United Kingdom.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 24.76 kDa 
• Atom Count: 1,945 
• Modeled Residue Count: 207 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SCML2 PROTEIN	A	221	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQR0 (Homo sapiens) Explore Q9UQR0  Go to UniProtKB:  Q9UQR0
PHAROS:  Q9UQR0 GTEx:  ENSG00000102098

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	B [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.204 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.762	α = 90
b = 47.696	β = 100.29
c = 41.493	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SOLVE/RESOLVE	phasing
CNS	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-15 
Deposition Author(s): Sathyamurthy, A., Allen, M.D., Murzin, A.G., Bycroft, M.

Revision History  

• Version 1.0: 2003-06-15
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Source and taxonomy
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Other