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: 43.58 kDa 
• Atom Count: 3381 
• Modelled Residue Count: 366 
• Deposited Residue Count: 376 
• Unique protein chains: 2

3IJ1

Crystal structure of Eed in complex with a trimethylated histone H4K20 peptide

• PDB DOI: 10.2210/pdb3IJ1/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-08-03 Released: 2009-09-15 
• Deposition Author(s): Justin, N., Sharpe, M.L., Martin, S., Taylor, W.R., De Marco, V., Gamblin, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.204 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

Role of the polycomb protein EED in the propagation of repressive histone marks.

Margueron, R., Justin, N., Ohno, K., Sharpe, M.L., Son, J., Drury, W.J., Voigt, P., Martin, S.R., Taylor, W.R., De Marco, V., Pirrotta, V., Reinberg, D., Gamblin, S.J.

(2009) Nature 461: 762-767

• PubMed: 19767730 
• DOI: 10.1038/nature08398
• Primary Citation of Related Structures:  
  3IIW, 3IIY, 3IJ0, 3IJ1, 3IJC


• PubMed Abstract: 
  

Polycomb group proteins have an essential role in the epigenetic maintenance of repressive chromatin states. The gene-silencing activity of the Polycomb repressive complex 2 (PRC2) depends on its ability to trimethylate lysine 27 of histone H3 (H3K27) by the catalytic SET domain of the EZH2 subunit, and at least two other subunits of the complex: SUZ12 and EED. Here we show that the carboxy-terminal domain of EED specifically binds to histone tails carrying trimethyl-lysine residues associated with repressive chromatin marks, and that this leads to the allosteric activation of the methyltransferase activity of PRC2. Mutations in EED that prevent it from recognizing repressive trimethyl-lysine marks abolish the activation of PRC2 in vitro and, in Drosophila, reduce global methylation and disrupt development. These findings suggest a model for the propagation of the H3K27me3 mark that accounts for the maintenance of repressive chromatin domains and for the transmission of a histone modification from mother to daughter cells.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Biochemistry, New York University Medical School, 522 First Avenue, New York, New York 10016, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polycomb protein EED	A	365	Homo sapiens	Mutation(s): 1  Gene Names: EED
UniProt & NIH Common Fund Data Resources
Find proteins for O75530 (Homo sapiens) Explore O75530  Go to UniProtKB:  O75530
PHAROS:  O75530

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4K20 peptide	B	11	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.204 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.55	α = 90
b = 85.321	β = 90
c = 91.229	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-08-03 
• Released Date: 2009-09-15 
Deposition Author(s): Justin, N., Sharpe, M.L., Martin, S., Taylor, W.R., De Marco, V., Gamblin, S.J.

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations