4WZR

Crystal structure of human Puf-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization.

Qiu, C.McCann, K.L.Wine, R.N.Baserga, S.J.Hall, T.M.

(2014) Proc Natl Acad Sci U S A 111: 18554-18559

  • DOI: https://doi.org/10.1073/pnas.1407634112
  • Primary Citation of Related Structures:  
    4WZR, 4WZW

  • PubMed Abstract: 

    Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins bind sequence specifically to mRNA targets using a single-stranded RNA-binding domain comprising eight Pumilio (PUM) repeats. PUM repeats have now been identified in proteins that function in pre-rRNA processing, including human Puf-A and yeast Puf6. This is a role not previously ascribed to PUF proteins. Here we present crystal structures of human Puf-A that reveal a class of nucleic acid-binding proteins with 11 PUM repeats arranged in an "L"-like shape. In contrast to classical PUF proteins, Puf-A forms sequence-independent interactions with DNA or RNA, mediated by conserved basic residues. We demonstrate that equivalent basic residues in yeast Puf6 are important for RNA binding, pre-rRNA processing, and mRNA localization. Thus, PUM repeats can be assembled into alternative folds that bind to structured nucleic acids in addition to forming canonical eight-repeat crescent-shaped RNA-binding domains found in classical PUF proteins.


  • Organizational Affiliation

    Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pumilio domain-containing protein KIAA0020
A, B
526Homo sapiensMutation(s): 2 
Gene Names: KIAA0020XTP5
UniProt & NIH Common Fund Data Resources
Find proteins for Q15397 (Homo sapiens)
Explore Q15397 
Go to UniProtKB:  Q15397
PHAROS:  Q15397
GTEx:  ENSG00000080608 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15397
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.495α = 90
b = 97.128β = 90
c = 282.801γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesIntramural Research Program

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references