5L80 | pdb_00005l80

Structure of Exuperantia EXO-like and SAM-like domains

• PDB DOI: https://doi.org/10.2210/pdb5L80/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-05 Released: 2016-07-06 
• Deposition Author(s): Lazzaretti, D., Veith, K., Bono, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.277 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.259 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Starting Model: experimental

Literature

The bicoid mRNA localization factor Exuperantia is an RNA-binding pseudonuclease.

Lazzaretti, D., Veith, K., Kramer, K., Basquin, C., Urlaub, H., Irion, U., Bono, F.

(2016) Nat Struct Mol Biol 23: 705-713

• PubMed: 27376588 
• DOI: https://doi.org/10.1038/nsmb.3254
• Primary Citation Related Structures: 
  5L7Z, 5L80


• PubMed Abstract: 
  

  Anterior patterning in Drosophila is mediated by the localization of bicoid (bcd) mRNA at the anterior pole of the oocyte. Exuperantia (Exu) is a putative exonuclease (EXO) associated with bcd and required for its localization. We present the crystal structure of Exu, which reveals a dimeric assembly with each monomer consisting of a 3'-5' EXO-like domain and a sterile alpha motif (SAM)-like domain. The catalytic site is degenerate and inactive. Instead, the EXO-like domain mediates dimerization and RNA binding. We show that Exu binds RNA directly in vitro, that the SAM-like domain is required for RNA binding activity and that Exu binds a structured element present in the bcd 3' untranslated region with high affinity. Through structure-guided mutagenesis, we show that Exu dimerization is essential for bcd localization. Our data demonstrate that Exu is a noncanonical RNA-binding protein with EXO-SAM-like domain architecture that interacts with its target RNA as a homodimer.

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Organizational Affiliation: 
• Max Planck Institute for Developmental Biology, Tübingen, Germany.
Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany.
Max Planck Institute of Biochemistry, Martinsried, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.4 kDa 
• Atom Count: 4,240 
• Modeled Residue Count: 570 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maternal protein exuperantia,Maternal protein exuperantia	A, B	353	Drosophila melanogaster	Mutation(s): 0  Gene Names: exu, CG8994
UniProt
Find proteins for P28750 (Drosophila melanogaster) Explore P28750  Go to UniProtKB:  P28750

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.277 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.259 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.54	α = 90
b = 66.59	β = 113.64
c = 81.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-06 
Deposition Author(s): Lazzaretti, D., Veith, K., Bono, F.

Revision History  

• Version 1.0: 2016-07-06
  Type: Initial release
  
• Version 1.1: 2016-07-13
  Changes: Database references
• Version 1.2: 2016-08-17
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description