6I1D

Structure of the Ysh1-Mpe1 nuclease complex from S.cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex.

Hill, C.H.Boreikaite, V.Kumar, A.Casanal, A.Kubik, P.Degliesposti, G.Maslen, S.Mariani, A.von Loeffelholz, O.Girbig, M.Skehel, M.Passmore, L.A.

(2019) Mol Cell 73: 1217-1231.e11

  • DOI: https://doi.org/10.1016/j.molcel.2018.12.023
  • Primary Citation of Related Structures:  
    6I1D

  • PubMed Abstract: 

    Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The cleavage reaction defines the 3' end of the mature mRNA, and thus the activity of the endonuclease is highly regulated. Here, we show that reconstitution of specific pre-mRNA cleavage with recombinant yeast proteins requires incorporation of the Ysh1 endonuclease into an eight-subunit "CPF core " complex. Cleavage also requires the accessory cleavage factors IA and IB, which bind substrate pre-mRNAs and CPF, likely facilitating assembly of an active complex. Using X-ray crystallography, electron microscopy, and mass spectrometry, we determine the structure of Ysh1 bound to Mpe1 and the arrangement of subunits within CPF core . Together, our data suggest that the active mRNA 3' end processing machinery is a dynamic assembly that is licensed to cleave only when all protein factors come together at the polyadenylation site.


  • Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease YSH1474Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: YSH1BRR5YLR277C
EC: 3.1.27
UniProt
Find proteins for Q06224 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q06224 
Go to UniProtKB:  Q06224
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06224
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein MPE1160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPE1YKL059CYKL316
UniProt
Find proteins for P35728 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35728 
Go to UniProtKB:  P35728
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35728
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.38α = 90
b = 124.27β = 103.21
c = 63.45γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
xia2data reduction
Cootmodel building
PHENIXmodel building
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilUnited Kingdom261151
European Research CouncilUnited Kingdom725685
Medical Research Council (United Kingdom)United KingdomMC_U105192715

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description