5JEA

Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7, bound to RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

Starting Model: experimental
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Literature

Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex.

Kowalinski, E.Kogel, A.Ebert, J.Reichelt, P.Stegmann, E.Habermann, B.Conti, E.

(2016) Mol Cell 63: 125-134

  • DOI: https://doi.org/10.1016/j.molcel.2016.05.028
  • Primary Citation of Related Structures:  
    5JEA

  • PubMed Abstract: 

    The RNA exosome complex associates with nuclear and cytoplasmic cofactors to mediate the decay, surveillance, or processing of a wide variety of transcripts. In the cytoplasm, the conserved core of the exosome (Exo10) functions together with the conserved Ski complex. The interaction of S. cerevisiae Exo10 and Ski is not direct but requires a bridging cofactor, Ski7. Here, we report the 2.65 Å resolution structure of S. cerevisiae Exo10 bound to the interacting domain of Ski7. Extensive hydrophobic interactions rationalize the high affinity and stability of this complex, pointing to Ski7 as a constitutive component of the cytosolic exosome. Despite the absence of sequence homology, cytoplasmic Ski7 and nuclear Rrp6 bind Exo10 using similar surfaces and recognition motifs. Knowledge of the interacting residues in the yeast complexes allowed us to identify a splice variant of human HBS1-Like as a Ski7-like exosome-binding protein, revealing the evolutionary conservation of this cytoplasmic cofactor.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP45305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
UniProt
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UniProt GroupQ05636
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component SKI6249Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
UniProt
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UniProt GroupP46948
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP43394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
UniProt
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP46226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
UniProt
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UniProt GroupP53256
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP42268Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42YDL111C
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UniProt GroupQ12277
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component MTR3250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3YGR158CG6676
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP40244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
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UniProt GroupQ08285
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component RRP4316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
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UniProt GroupP38792
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex component CSL4295Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS31,005Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIS3RRP44YOL021CO2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Superkiller protein 7,Endolysin279Saccharomyces cerevisiae S288CTequatrovirus T4
This entity is chimeric
Mutation(s): 0 
Gene Names: SKI7YOR076CYOR29-27
EC: 3.2.1.17
UniProt
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Find proteins for P00720 (Enterobacteria phage T4)
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UniProt GroupsP00720Q08491
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Entity ID: 12
MoleculeChains LengthOrganismImage
RNA (29-MER)L [auth R]46synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
M [auth A]
N [auth A]
Q [auth C]
R [auth D]
T [auth G]
M [auth A],
N [auth A],
Q [auth C],
R [auth D],
T [auth G],
U [auth G],
V [auth J]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
W [auth J]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth B],
P [auth B],
S [auth F],
X [auth J]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.08α = 90
b = 182.53β = 90
c = 250.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilGermany294371
German Research FoundationGermanySFB646
German Research FoundationGermanySFB1035
German Research FoundationGermanyGRK1721
German Research FoundationGermanyFOR1680
German Research FoundationGermanyCIPSM

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Atomic model, Database references
  • Version 1.2: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Refinement description