Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 36.53 kDa 
• Atom Count: 2645 
• Residue Count: 310 
• Unique protein chains: 2

4A7J

Symmetric Dimethylation of H3 Arginine 2 is a Novel Histone Mark that Supports Euchromatin Maintenance

• DOI: 10.2210/pdb4A7J/pdb

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


• Deposited: 2011-11-14 Released: 2012-01-11 
• Deposition Author(s): Migliori, V., Muller, J., Phalke, S., Low, D., Bezzi, M., ChuenMok, W., Gunaratne, J., Capasso, P., Bassi, C., Cecatiello, V., DeMarco, A., Blackstock, W., Kuznetsov, V., Amati, B., Mapelli, M., Guccione, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Symmetric Dimethylation of H3R2 is a Newly Identified Histone Mark that Supports Euchromatin Maintenance

Migliori, V., Muller, J., Phalke, S., Low, D., Bezzi, M., Chuenmok, W., Sahu, S.K., Gunaratne, J., Capasso, P., Bassi, C., Cecatiello, V., Demarco, A., Blackstock, W., Kuznetsov, V., Amati, B., Mapelli, M., Guccione, E.

(2012) Nat Struct Mol Biol 19: 136

• PubMed: 22231400 
• DOI: 10.1038/nsmb.2209
• Primary Citation of Related Structures:  
  4A7J


• PubMed Abstract: 
  

The asymmetric dimethylation of histone H3 arginine 2 (H3R2me2a) acts as a repressive mark that antagonizes trimethylation of H3 lysine 4. Here we report that H3R2 is also symmetrically dimethylated (H3R2me2s) by PRMT5 and PRMT7 and present in euchromatic regions. Profiling of H3-tail interactors by SILAC MS revealed that H3R2me2s excludes binding of RBBP7, a central component of co-repressor complexes Sin3a, NURD and PRC2. Conversely H3R2me2s enhances binding of WDR5, a common component of the coactivator complexes MLL, SET1A, SET1B, NLS1 and ATAC. The interaction of histone H3 with WDR5 distinguishes H3R2me2s from H3R2me2a, which impedes the recruitment of WDR5 to chromatin. The crystallographic structure of WDR5 and the H3R2me2s peptide elucidates the molecular determinants of this high affinity interaction. Our findings identify H3R2me2s as a previously unknown mark that keeps genes poised in euchromatin for transcriptional activation upon cell-cycle withdrawal and differentiation in human cells.

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Organizational Affiliation: 

Institute of Molecular and Cell Biology, Singapore.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3.1T	B	16	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431 GTEx  ENSG00000197409GTEx  ENSG00000197153GTEx  ENSG00000278828GTEx  ENSG00000275714GTEx  ENSG00000273983GTEx  ENSG00000274750GTEx  ENSG00000275379GTEx  ENSG00000277775

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD REPEAT-CONTAINING PROTEIN 5	A	318	Homo sapiens	Mutation(s): 0  Gene Names: WDR5, BIG3
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
NIH Common Fund Data Resources
PHAROS  P61964 GTEx  ENSG00000196363

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2MR	B	L-PEPTIDE LINKING	C8 H18 N4 O2		ARG

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.222 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.6	α = 90
b = 46.8	β = 104.33
c = 65	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-14 
• Released Date: 2012-01-11 
Deposition Author(s): Migliori, V., Muller, J., Phalke, S., Low, D., Bezzi, M., ChuenMok, W., Gunaratne, J., Capasso, P., Bassi, C., Cecatiello, V., DeMarco, A., Blackstock, W., Kuznetsov, V., Amati, B., Mapelli, M., Guccione, E.

Revision History 

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2012-02-15
  Changes: Other