Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.22 kDa 
• Atom Count: 2974 
• Modelled Residue Count: 356 
• Deposited Residue Count: 407 
• Unique protein chains: 1

1S4U

Crystal Structure analysis of the beta-propeller protein Ski8p

• PDB DOI: 10.2210/pdb1S4U/pdb

• Classification: ANTIVIRAL PROTEIN
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-18 Released: 2004-12-28 
• Deposition Author(s): Cheng, Z., Song, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.283 
• R-Value Work: 0.251 
• R-Value Observed: 0.253 

Literature

Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recombination

Cheng, Z., Liu, Y., Wang, C., Parker, R., Song, H.

(2004) Protein Sci 13: 2673-2684

• PubMed: 15340168 
• DOI: 10.1110/ps.04856504
• Primary Citation of Related Structures:  
  1S4U


• PubMed Abstract: 
  

Ski8p is a WD-repeat protein with an essential role for the Ski complex assembly in an exosome-dependent 3'-to-5' mRNA decay. In addition, Ski8p is involved in meiotic recombination by interacting with Spo11p protein. We have determined the crystal structure of Ski8p from Saccharomyces cerevisiae at 2.2 A resolution. The structure reveals that Ski8p folds into a seven-bladed beta propeller. Mapping sequence conservation and hydrophobicities of amino acids on the molecular surface of Ski8p reveals a prominent site on the top surface of the beta propeller, which is most likely involved in mediating interactions of Ski8p with Ski3p and Spo11p. Mutagenesis combined with yeast two-hybrid and GST pull-down assays identified the top surface of the beta propeller as being required for Ski8p binding to Ski3p and Spo11p. The functional implications for Ski8p function in both mRNA decay and meiotic recombination are discussed.

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Organizational Affiliation: 

Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiviral protein SKI8	A [auth X]	407	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SKI8, YGL213C
UniProt
Find proteins for Q02793 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02793  Go to UniProtKB:  Q02793

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.283 
• R-Value Work: 0.251 
• R-Value Observed: 0.253 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.555	α = 90
b = 66.791	β = 90
c = 81.459	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-18 
• Released Date: 2004-12-28 
Deposition Author(s): Cheng, Z., Song, H.

Revision History  

• Version 1.0: 2004-12-28
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance