4KUL

Crystal structure of N-terminal acetylated yeast Sir3 BAH domain V83P mutant

• PDB DOI: https://doi.org/10.2210/pdb4KUL/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-05-22 Released: 2013-08-07 
• Deposition Author(s): Yang, D., Fang, Q., Wang, M., Ren, R., Wang, H., He, M., Sun, Y., Yang, N., Xu, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

N alpha-acetylated Sir3 stabilizes the conformation of a nucleosome-binding loop in the BAH domain.

Yang, D., Fang, Q., Wang, M., Ren, R., Wang, H., He, M., Sun, Y., Yang, N., Xu, R.M.

(2013) Nat Struct Mol Biol 20: 1116-1118

• PubMed: 23934152 
• DOI: https://doi.org/10.1038/nsmb.2637
• Primary Citation of Related Structures:  
  4KUD, 4KUI, 4KUL


• PubMed Abstract: 
  

  In Saccharomyces cerevisiae, acetylation of the Sir3 N terminus is important for transcriptional silencing. This covalent modification promotes the binding of the Sir3 BAH domain to the nucleosome, but a mechanistic understanding of this phenomenon is lacking. By X-ray crystallography, we show here that the acetylated N terminus of Sir3 does not interact with the nucleosome directly. Instead, it stabilizes a nucleosome-binding loop in the BAH domain.

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Organizational Affiliation: 

1] National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [2] University of Chinese Academy of Sciences, Beijing, China. [3].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.77 kDa 
• Atom Count: 1,654 
• Modelled Residue Count: 193 
• Deposited Residue Count: 224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulatory protein SIR3	A	224	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: SIR3, CMT1, MAR2, STE8, YLR442C, L9753.10
UniProt
Find proteins for P06701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06701  Go to UniProtKB:  P06701

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AYA	A	L-PEPTIDE LINKING	C5 H9 N O3		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.277 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.227	α = 90
b = 43.453	β = 97.43
c = 53.636	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Yang, D., Fang, Q., Wang, M., Ren, R., Wang, H., He, M., Sun, Y., Yang, N., Xu, R.M.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2013-09-04
  Changes: Database references
• Version 1.2: 2022-08-24
  Changes: Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Refinement description