3BSB

Crystal Structure of Human Pumilio1 in Complex with CyclinB reverse RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of human Pumilio with noncognate RNAs reveal molecular mechanisms for binding promiscuity.

Gupta, Y.K.Nair, D.T.Wharton, R.P.Aggarwal, A.K.

(2008) Structure 16: 549-557

  • DOI: 10.1016/j.str.2008.01.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence sh ...

    Pumilio is a founder member of the evolutionarily conserved Puf family of RNA-binding proteins that control a number of physiological processes in eukaryotes. A structure of human Pumilio (hPum) Puf domain bound to a Drosophila regulatory sequence showed that each Puf repeat recognizes a single nucleotide. Puf domains in general bind promiscuously to a large set of degenerate sequences, but the structural basis for this promiscuity has been unclear. Here, we describe the structures of hPum Puf domain complexed to two noncognate RNAs, CycB(reverse) and Puf5. In each complex, one of the nucleotides is ejected from the binding surface, in effect, acting as a "spacer." The complexes also reveal the plasticity of several Puf repeats, which recognize noncanonical nucleotides. Together, these complexes provide a molecular basis for recognition of degenerate binding sites, which significantly increases the number of mRNAs targeted for regulation by Puf proteins in vivo.


    Organizational Affiliation

    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pumilio homolog 1
A, B
343Homo sapiensMutation(s): 0 
Gene Names: PUM1 (KIAA0099, PUMH1)
Find proteins for Q14671 (Homo sapiens)
Go to Gene View: PUM1
Go to UniProtKB:  Q14671
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*UP*UP*UP*AP*AP*UP*GP*UP*U)-3'C9N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 35.874α = 90.00
b = 64.292β = 90.00
c = 321.230γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
MAR345data collection
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description