5OKZ

Crystal Strucrure of the Mpp6 Exosome complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase.

Falk, S.Bonneau, F.Ebert, J.Kogel, A.Conti, E.

(2017) Cell Rep 20: 2279-2286

  • DOI: 10.1016/j.celrep.2017.08.033
  • Primary Citation of Related Structures:  
    5OKZ

  • PubMed Abstract: 
  • The RNA-degrading exosome mediates the processing and decay of many cellular transcripts. In the yeast nucleus, the ubiquitous 10-subunit exosome core complex (Exo-9-Rrp44) functions with four conserved cofactors (Rrp6, Rrp47, Mtr4, and Mpp6). Biochemical and structural studies to date have shed insights into the mechanisms of the exosome core and its nuclear cofactors, with the exception of Mpp6 ...

    The RNA-degrading exosome mediates the processing and decay of many cellular transcripts. In the yeast nucleus, the ubiquitous 10-subunit exosome core complex (Exo-9-Rrp44) functions with four conserved cofactors (Rrp6, Rrp47, Mtr4, and Mpp6). Biochemical and structural studies to date have shed insights into the mechanisms of the exosome core and its nuclear cofactors, with the exception of Mpp6. We report the 3.2-Å resolution crystal structure of a S. cerevisiae Exo-9-Mpp6 complex, revealing how linear motifs in the Mpp6 middle domain bind Rrp40 via evolutionary conserved residues. In particular, Mpp6 binds near a tryptophan residue of Rrp40 that is mutated in human patients suffering from pontocerebellar hypoplasia. Using biochemical assays, we show that Mpp6 is required for the ability of Mtr4 to extend the trajectory of an RNA entering the exosome core, suggesting that it promotes the channeling of substrates from the nuclear helicase to the processive RNase.


    Organizational Affiliation

    Max-Planck-Institute of Biochemistry, Department of Structural Cell Biology, Am Klopferspitz 18, 82152 Martinsried/Munich, Germany. Electronic address: conti@biochem.mpg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4J [auth I], T [auth S], DA [auth c], A [auth m]295Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP45B [auth A], L [auth K], V [auth U], FA [auth e]305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component SKI6C [auth B], M [auth L], W [auth V], GA [auth f]249Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43D [auth C], N [auth M], X [auth W], HA [auth g]394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46E [auth D], O [auth N], Y [auth X], IA [auth h]226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42F [auth E], P [auth O], Z [auth Y], JA [auth i]268Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42YDL111C
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3G [auth F], Q [auth P], AA [auth Z], KA [auth j]250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3YGR158CG6676
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40H [auth G], R [auth Q], BA [auth a], LA [auth k]244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4I [auth H], S [auth R], CA [auth b], MA [auth l]316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
M-phase phosphoprotein 6 homologK [auth J], U [auth T], EA [auth d], NA [auth n]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP6YNR024WN3230
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.779α = 90
b = 237.43β = 110.37
c = 201.895γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata processing
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium294371
German Research FoundationGermanySFB1035
German Research FoundationGermanyGRK1721
German Research FoundationGermanyCluster of Excellence CIPSM

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references