Two Tandem RRM Domains of FBP-Interacting Repressor (FIR), also Known as PUF60

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.239 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Unraveling the mechanism of recognition of the 3' splice site of the adenovirus major late promoter intron by the alternative splicing factor PUF60.

Hsiao, H.T.Crichlow, G.V.Murphy, J.W.Folta-Stogniew, E.J.Lolis, E.J.Braddock, D.T.

(2020) PLoS One 15: e0242725-e0242725

  • DOI: https://doi.org/10.1371/journal.pone.0242725
  • Primary Citation of Related Structures:  
    5KVY, 5KW1, 5KW6, 5KWQ

  • PubMed Abstract: 

    Pre-mRNA splicing is critical for achieving required amounts of a transcript at a given time and for regulating production of encoded protein. A given pre-mRNA may be spliced in many ways, or not at all, giving rise to multiple gene products. Numerous splicing factors are recruited to pre-mRNA splice sites to ensure proper splicing. One such factor, the 60 kDa poly(U)-binding splicing factor (PUF60), is recruited to sites that are not always spliced, but rather function as alternative splice sites. In this study, we characterized the interaction of PUF60 with a splice site from the adenovirus major late promoter (the AdML 3' splice site, AdML3'). We found that the PUF60-AdML3' dissociation constants are in the micromolar range, with the binding affinity predominantly provided by PUF60's two central RNA recognition motifs (RRMs). A 1.95 Å crystal structure of the two PUF60 RRMs in complex with AdML3' revealed a dimeric organization placing two stretches of nucleic acid tracts in opposing directionalities, which can cause looping of nucleic acid and explain how PUF60 affects pre-mRNA geometry to effect splicing. Solution characterization of this complex by light-scattering and UV/Vis spectroscopy suggested a potential 2:1 (PUF602:AdML3') stoichiometry, consistent with the crystal structure. This work defines the sequence specificity of the alternative splicing factor PUF60 at the pre-mRNA 3' splice site. Our observations suggest that control of pre-mRNA directionality is important in the early stage of spliceosome assembly, and advance our understanding of the molecular mechanism by which alternative and constitutive splicing factors differentiate among 3' splice sites.

  • Organizational Affiliation

    Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly(U)-binding-splicing factor PUF60
A, B
216Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHX1 (Homo sapiens)
Explore Q9UHX1 
Go to UniProtKB:  Q9UHX1
GTEx:  ENSG00000179950 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHX1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.239 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.831α = 90
b = 61.831β = 90
c = 80.412γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
American Cancer SocietyUnited StatesRSG-0-222-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2020-12-09
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description