8OIJ

Drosophila Smaug-Smoothened complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.274 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for binding of Drosophila Smaug to the GPCR Smoothened and to the germline inducer Oskar.

Kubikova, J.Ubartaite, G.Metz, J.Jeske, M.

(2023) Proc Natl Acad Sci U S A 120: e2304385120-e2304385120

  • DOI: https://doi.org/10.1073/pnas.2304385120
  • Primary Citation of Related Structures:  
    8OIJ, 8OIK

  • PubMed Abstract: 

    Drosophila Smaug and its orthologs comprise a family of mRNA repressor proteins that exhibit various functions during animal development. Smaug proteins contain a characteristic RNA-binding sterile-α motif (SAM) domain and a conserved but uncharacterized N-terminal domain (NTD). Here, we resolved the crystal structure of the NTD of the human SAM domain-containing protein 4A (SAMD4A, a.k.a. Smaug1) to 1.6 Å resolution, which revealed its composition of a homodimerization D subdomain and a subdomain with similarity to a pseudo-HEAT-repeat analogous topology (PHAT) domain. Furthermore, we show that Drosophila Smaug directly interacts with the Drosophila germline inducer Oskar and with the Hedgehog signaling transducer Smoothened through its NTD. We determined the crystal structure of the NTD of Smaug in complex with a Smoothened α-helical peptide to 2.0 Å resolution. The peptide binds within a groove that is formed by both the D and PHAT subdomains. Structural modeling supported by experimental data suggested that an α-helix within the disordered region of Oskar binds to the NTD of Smaug in a mode similar to Smoothened. Together, our data uncover the NTD of Smaug as a peptide-binding domain.


  • Organizational Affiliation

    Biochemistry Center, Heidelberg University, Heidelberg 69120, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Smaug
A, B
177Drosophila melanogasterMutation(s): 0 
Gene Names: smgCG5263
UniProt
Find proteins for Q23972 (Drosophila melanogaster)
Explore Q23972 
Go to UniProtKB:  Q23972
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ23972
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein smoothened
C, D
35Drosophila melanogasterMutation(s): 0 
Gene Names: smoCG11561
UniProt
Find proteins for P91682 (Drosophila melanogaster)
Explore P91682 
Go to UniProtKB:  P91682
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP91682
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.274 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.59α = 90
b = 76.59β = 90
c = 268.47γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MxCuBEdata collection
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references