3MDI

Crystal Structure of the 25kDa Subunit of Human Cleavage factor Im in complex with RNA UGUAAA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing.

Yang, Q.Gilmartin, G.M.Doublie, S.

(2010) Proc Natl Acad Sci U S A 107: 10062-10067

  • DOI: 10.1073/pnas.1000848107
  • Primary Citation of Related Structures:  
    3MDG, 3MDI

  • PubMed Abstract: 
  • Human Cleavage Factor Im (CFI(m)) is an essential component of the pre-mRNA 3' processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conse ...

    Human Cleavage Factor Im (CFI(m)) is an essential component of the pre-mRNA 3' processing complex that functions in the regulation of poly(A) site selection through the recognition of UGUA sequences upstream of the poly(A) site. Although the highly conserved 25 kDa subunit (CFI(m)25) of the CFI(m) complex possesses a characteristic alpha/beta/alpha Nudix fold, CFI(m)25 has no detectable hydrolase activity. Here we report the crystal structures of the human CFI(m)25 homodimer in complex with UGUAAA and UUGUAU RNA sequences. CFI(m)25 is the first Nudix protein to be reported to bind RNA in a sequence-specific manner. The UGUA sequence contributes to binding specificity through an intramolecular G:A Watson-Crick/sugar-edge base interaction, an unusual pairing previously found to be involved in the binding specificity of the SAM-III riboswitch. The structures, together with mutational data, suggest a novel mechanism for the simultaneous sequence-specific recognition of two UGUA elements within the pre-mRNA. Furthermore, the mutually exclusive binding of RNA and the signaling molecule Ap(4)A (diadenosine tetraphosphate) by CFI(m)25 suggests a potential role for small molecules in the regulation of mRNA 3' processing.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, Stafford Hall, University of Vermont, Burlington, VT 05405, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cleavage and polyadenylation specificity factor subunit 5 AB227Homo sapiensMutation(s): 0 
Gene Names: CFIM25CPSF25CPSF5NUDT21
Find proteins for O43809 (Homo sapiens)
Explore O43809 
Go to UniProtKB:  O43809
NIH Common Fund Data Resources
PHAROS:  O43809
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*GP*UP*AP*AP*A)-3')C6N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    A, B
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.07 Å
    • R-Value Free: 0.233 
    • R-Value Work: 0.180 
    • R-Value Observed: 0.183 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 71.362α = 90
    b = 72.037β = 90
    c = 96.16γ = 90
    Software Package:
    Software NamePurpose
    XSCALEdata scaling
    PHENIXrefinement
    PDB_EXTRACTdata extraction
    XDSdata scaling
    XDSdata reduction
    MOLREPphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2010-06-02
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance