Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 66.09 kDa 
• Atom Count: 3497 
• Modelled Residue Count: 455 
• Deposited Residue Count: 586 
• Unique protein chains: 2

4C5H

Crystal structure of the minimal Pho-Sfmbt complex (P3121 spacegroup)

• PDB DOI: 10.2210/pdb4C5H/pdb

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


• Deposited: 2013-09-11 Released: 2013-11-13 
• Deposition Author(s): Alfieri, C., Glatt, S., Mueller, C.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Literature

Structural Basis for Targeting the Chromatin Repressor Sfmbt to Polycomb Response Elements

Alfieri, C., Gambetta, M.C., Matos, R., Glatt, S., Sehr, P., Fraterman, S., Wilm, M., Mueller, J., Mueller, C.W.

(2013) Genes Dev 27: 2367

• PubMed: 24186981 
• DOI: 10.1101/gad.226621.113
• Primary Citation of Related Structures:  
  4C5E, 4C5G, 4C5H, 4C5I


• PubMed Abstract: 
  

Polycomb group (PcG) protein complexes repress developmental regulator genes by modifying their chromatin. How different PcG proteins assemble into complexes and are recruited to their target genes is poorly understood. Here, we report the crystal structure of the core of the Drosophila PcG protein complex Pleiohomeotic (Pho)-repressive complex (PhoRC), which contains the Polycomb response element (PRE)-binding protein Pho and Sfmbt. The spacer region of Pho, separated from the DNA-binding domain by a long flexible linker, forms a tight complex with the four malignant brain tumor (4MBT) domain of Sfmbt. The highly conserved spacer region of the human Pho ortholog YY1 binds three of the four human 4MBT domain proteins in an analogous manner but with lower affinity. Comparison of the Drosophila Pho:Sfmbt and human YY1:MBTD1 complex structures provides a molecular explanation for the lower affinity of YY1 for human 4MBT domain proteins. Structure-guided mutations that disrupt the interaction between Pho and Sfmbt abolish formation of a ternary Sfmbt:Pho:DNA complex in vitro and repression of developmental regulator genes in Drosophila. PRE tethering of Sfmbt by Pho is therefore essential for Polycomb repression in Drosophila. Our results support a model where DNA tethering of Sfmbt by Pho and multivalent interactions of Sfmbt with histone modifications and other PcG proteins create a hub for PcG protein complex assembly at PREs.

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Organizational Affiliation: 

European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYCOMB PROTEIN SFMBT	A	451	Drosophila melanogaster	Mutation(s): 0  Gene Names: Sfmbt, CG16975
UniProt
Find proteins for Q9VK33 (Drosophila melanogaster) Explore Q9VK33  Go to UniProtKB:  Q9VK33

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYCOMB PROTEIN PHO	B	135	Drosophila melanogaster	Mutation(s): 0  Gene Names: pho, CG17743
UniProt
Find proteins for Q8ST83 (Drosophila melanogaster) Explore Q8ST83  Go to UniProtKB:  Q8ST83

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.234 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.78	α = 90
b = 120.78	β = 90
c = 153.02	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-11 
• Released Date: 2013-11-13 
Deposition Author(s): Alfieri, C., Glatt, S., Mueller, C.W.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release