3BSX

Crystal Structure of Human Pumilio 1 in complex with Puf5 RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.218 

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This is version 1.1 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:  
    3BSB, 3BSX

  • 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 showed that each Puf repeat recognizes a single nucleotide ...

    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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Pumilio homolog 1C [auth A],
D [auth B]
343Homo sapiensMutation(s): 0 
Gene Names: PUM1KIAA0099PUMH1
UniProt & NIH Common Fund Data Resources
Find proteins for Q14671 (Homo sapiens)
Explore Q14671 
Go to UniProtKB:  Q14671
PHAROS:  Q14671
GTEx:  ENSG00000134644 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14671
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*UP*UP*GP*UP*AP*AP*UP*AP*UP*UP*A)-3'A [auth C],
B [auth D]
11N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.835α = 90
b = 65.642β = 90
c = 313.975γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance