2RSN | pdb_00002rsn

Solution structure of the chromodomain of Chp1 in complex with H3K9me3 peptide

• PDB DOI: https://doi.org/10.2210/pdb2RSN/pdb
• BMRB: 11496

• Classification: NUCLEAR PROTEIN
• Organism(s): Schizosaccharomyces pombe 972h-, Schizosaccharomyces pombe
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-04-18 Released: 2012-08-29 
• Deposition Author(s): Shimojo, H., Nishimura, Y.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing

Ishida, M., Shimojo, H., Hayashi, A., Kawaguchi, R., Ohtani, Y., Uegaki, K., Nishimura, Y., Nakayama, J.

(2012) Mol Cell 47: 228-241

• PubMed: 22727667 
• DOI: https://doi.org/10.1016/j.molcel.2012.05.017
• Primary Citation Related Structures: 
  2RSN, 2RSO


• PubMed Abstract: 
  

  Centromeric heterochromatin assembly in fission yeast requires the RNAi pathway. Chp1, a chromodomain (CD) protein, forms the Ago1-containing RNA-induced transcriptional silencing (RITS) complex and recruits siRNA-bound RITS to methylated histone H3 lysine 9 (H3K9me) via its CD. Here, we show that the CD of Chp1 (Chp1-CD) possesses unique nucleic acid-binding activities that are essential for heterochromatic gene silencing. Detailed electrophoretic-mobility shift analyses demonstrated that Chp1 binds to RNA via the CD in addition to its central RNA-recognition motif. Interestingly, robust RNA- and DNA-binding activity of Chp1-CD was strongly enhanced when it was bound to H3K9me, which was revealed to involve a positively charged domain within the Chp1-CD by structural analyses. These results demonstrate a role for the CD that provides a link between RNA, DNA, and methylated histone tails to ensure heterochromatic gene silencing.

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Organizational Affiliation: 
• Laboratory for Chromatin Dynamics, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.94 kDa 
• Atom Count: 772 
• Modeled Residue Count: 93 
• Deposited Residue Count: 93 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromo domain-containing protein 1	A	75	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: chp1
UniProt
Find proteins for Q10103 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q10103  Go to UniProtKB:  Q10103

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide from Histone H3	B	18	Schizosaccharomyces pombe	Mutation(s): 0
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61830  Go to UniProtKB:  P61830

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
M3L	B	LYS	Methylation	C9 H21 N2 O2

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Shimojo, H., Nishimura, Y.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary