2RSO | pdb_00002rso

Solution structure of the chromodomain of Swi6

• PDB DOI: https://doi.org/10.2210/pdb2RSO/pdb
• BMRB: 11497

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


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

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 600 
• Conformers Submitted: 20 
• Selection Criteria: target function 

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.

---

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: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.5 kDa 
• Atom Count: 735 
• Modeled Residue Count: 92 
• Deposited Residue Count: 92 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin-associated protein swi6	A	92	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: swi6
UniProt
Find proteins for P40381 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P40381  Go to UniProtKB:  P40381

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 600 
• Conformers Submitted: 20 
• Selection Criteria: target function 

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: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references