4BUJ

Crystal structure of the S. cerevisiae Ski2-3-8 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex.

Halbach, F.Reichelt, P.Rode, M.Conti, E.

(2013) Cell 154: 814

  • DOI: 10.1016/j.cell.2013.07.017
  • Primary Citation of Related Structures:  
    4BUJ

  • PubMed Abstract: 
  • The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry. The crystal structure of an S ...

    The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry. The crystal structure of an S. cerevisiae 370 kDa core complex shows that Ski3 forms an array of 33 TPR motifs organized in N-terminal and C-terminal arms. The C-terminal arm of Ski3 and the two Ski8 subunits position the helicase core of Ski2 centrally within the complex, enhancing RNA binding. The Ski3 N-terminal arm and the Ski2 insertion domain allosterically modulate the ATPase and helicase activities of the complex. Biochemical data suggest that the Ski complex can thread RNAs directly to the exosome, coupling the helicase and the exoribonuclease through a continuous RNA channel. Finally, we identify a Ski8-binding motif common to Ski3 and Spo11, rationalizing the moonlighting properties of Ski8 in mRNA decay and meiosis.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried/Munich, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIVIRAL HELICASE SKI2A, E1044Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI2YLR398CL8084.17
EC: 3.6.4.13
Find proteins for P35207 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35207 
Go to UniProtKB:  P35207
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUPERKILLER PROTEIN 3B, F1436Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI3YPR189WP9677.7
Find proteins for P17883 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17883 
Go to UniProtKB:  P17883
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ANTIVIRAL PROTEIN SKI8C, D, G, H397Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI8REC103YGL213C
Find proteins for Q02793 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q02793 
Go to UniProtKB:  Q02793
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth H] , BA [auth H] , I [auth A] , J [auth A] , K [auth A] , L [auth A] , M [auth B] , N [auth C] , 
AA [auth H],  BA [auth H],  I [auth A],  J [auth A],  K [auth A],  L [auth A],  M [auth B],  N [auth C],  O [auth C],  P [auth C],  Q [auth C],  R [auth D],  S [auth D],  T [auth E],  U [auth E],  V [auth E],  W [auth G],  X [auth G],  Y [auth G],  Z [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.375α = 90
b = 200.415β = 90
c = 340.179γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other, Refinement description