1OXJ | pdb_00001oxj

Crystal structure of the Smaug RNA binding domain

• PDB DOI: https://doi.org/10.2210/pdb1OXJ/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2003-04-02 Released: 2003-07-08 
• Deposition Author(s): Green, J.B., Gardner, C.D., Wharton, R.P., Aggarwal, A.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.244 (Depositor) 
• R-Value Work: 
  0.229 (Depositor) 
• R-Value Observed: 
  0.231 (Depositor) 

Literature

RNA recognition via the SAM domain of Smaug.

Green, J.B., Gardner, C.D., Wharton, R.P., Aggarwal, A.K.

(2003) Mol Cell 11: 1537-1548

• PubMed: 12820967 
• DOI: https://doi.org/10.1016/s1097-2765(03)00178-3
• Primary Citation Related Structures: 
  1OXJ


• PubMed Abstract: 
  

  The Nanos protein gradient in Drosophila, required for proper abdominal segmentation, is generated in part via translational repression of its mRNA by Smaug. We report here the crystal structure of the Smaug RNA binding domain, which shows no sequence homology to any previously characterized RNA binding motif. The structure reveals an unusual makeup in which a SAM domain, a common protein-protein interaction module, is affixed to a pseudo-HEAT repeat analogous topology (PHAT) domain. Unexpectedly, we find through a combination of structural and genetic analysis that it is primarily the SAM domain that interacts specifically with the appropriate nanos mRNA regulatory sequence. Therefore, in addition to their previously characterized roles in protein-protein interactions, some SAM domains play crucial roles in RNA binding.

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Organizational Affiliation: 
• Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.68 kDa 
• Atom Count: 1,518 
• Modeled Residue Count: 170 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-binding protein Smaug	A	173	Drosophila melanogaster	Mutation(s): 0  Gene Names: SMG
UniProt
Find proteins for Q23972 (Drosophila melanogaster) Explore Q23972  Go to UniProtKB:  Q23972

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.244 (Depositor) 
• R-Value Work:  0.229 (Depositor) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.32	α = 90
b = 129.32	β = 90
c = 33.125	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-08 
Deposition Author(s): Green, J.B., Gardner, C.D., Wharton, R.P., Aggarwal, A.K.

Revision History  

• Version 1.0: 2003-07-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references