5KLA

Crystal structure of the drosophila Pumilio RNA-binding domain in complex with hunchback RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio.

Weidmann, C.A.Qiu, C.Arvola, R.M.Lou, T.F.Killingsworth, J.Campbell, Z.T.Tanaka Hall, T.M.Goldstrohm, A.C.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.17096
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Collaboration among the multitude of RNA-binding proteins (RBPs) is ubiquitous, yet our understanding of these key regulatory complexes has been limited to single RBPs. We investigated combinatorial translational regulation by Drosophila Pumilio (Pum ...

    Collaboration among the multitude of RNA-binding proteins (RBPs) is ubiquitous, yet our understanding of these key regulatory complexes has been limited to single RBPs. We investigated combinatorial translational regulation by Drosophila Pumilio (Pum) and Nanos (Nos), which control development, fertility, and neuronal functions. Our results show how the specificity of one RBP (Pum) is modulated by cooperative RNA recognition with a second RBP (Nos) to synergistically repress mRNAs. Crystal structures of Nos-Pum-RNA complexes reveal that Nos embraces Pum and RNA, contributes sequence-specific contacts, and increases Pum RNA-binding affinity. Nos shifts the recognition sequence and promotes repression complex formation on mRNAs that are not stably bound by Pum alone, explaining the preponderance of sub-optimal Pum sites regulated in vivo. Our results illuminate the molecular mechanism of a regulatory switch controlling crucial gene expression programs, and provide a framework for understanding how the partnering of RBPs evokes changes in binding specificity that underlie regulatory network dynamics.


    Organizational Affiliation

    Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States.,Epigenetics and Stem Cell Biology Laboratory, National Institutes of Health, Research Triangle Park, United States.,Department of Biological Sciences, University of Texas at Dallas, Richardson, United States.,National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States.,Department of Biological Chemistry, University of Michigan, Ann Arbor, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maternal protein pumilio
A
337Drosophila melanogasterMutation(s): 0 
Gene Names: pum
Find proteins for P25822 (Drosophila melanogaster)
Go to UniProtKB:  P25822
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*UP*GP*UP*AP*CP*AP*UP*A)-3')B8Drosophila melanogaster
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 194.904α = 90.00
b = 29.537β = 101.25
c = 62.034γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-23 
  • Released Date: 2016-08-17 
  • Deposition Author(s): Qiu, C., Hall, T.M.T.

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-08-24
    Type: Database references