8OIK

D-PHAT domain (NTD) of human SAMD4A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 homolog 1
A, B, C
180Homo sapiensMutation(s): 0 
Gene Names: SAMD4AKIAA1053SAMD4SMAUG1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPU9 (Homo sapiens)
Explore Q9UPU9 
Go to UniProtKB:  Q9UPU9
PHAROS:  Q9UPU9
GTEx:  ENSG00000020577 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPU9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.829α = 90
b = 142.786β = 90
c = 137.096γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
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: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Derived calculations
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references