1MFK | pdb_00001mfk

Structure of Prokaryotic SECIS mRNA Hairpin

• PDB DOI: https://doi.org/10.2210/pdb1MFK/pdb
• NAKB: 1MFK

• Classification: RNA
• Mutation(s): No 


• Deposited: 2002-08-12 Released: 2002-11-13 
• Deposition Author(s): Fourmy, D., Guittet, E., Yoshizawa, S.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Structure of Prokaryotic SECIS mRNA Hairpin and its Interaction with Elongation Factor SELB

Fourmy, D., Guittet, E., Yoshizawa, S.

(2002) J Mol Biology 324: 137-150

• PubMed: 12421564 
• DOI: https://doi.org/10.1016/s0022-2836(02)01030-6
• Primary Citation Related Structures: 
  1MFK


• PubMed Abstract: 
  

  In prokaryotes, the recoding of a UGA stop codon as a selenocysteine codon requires a special elongation factor (EF) SelB and a stem-loop structure within the mRNA called a selenocysteine insertion sequence (SECIS). Here, we used NMR spectroscopy to determine the solution structure of the SECIS mRNA hairpin and characterized its interaction with the mRNA-binding domain of SelB. Our structural and biochemical data identified the conserved structural features important for binding to EF SelB within different SECIS RNA sequences. In the free SECIS mRNA structure, conserved nucleotides are strongly exposed for recognition by SelB. Binding of the C-terminal domain of SelB stabilizes the RNA secondary structure. In the protein-RNA complex, a Watson-Crick loop base-pair leaves a GpU sequence accessible for SelB recognition. This GpU sequence at the tip of the capping tetraloop and a bulge uracil five Watson-Crick base-pairs apart from the GpU are essential for interaction with SelB.

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Organizational Affiliation: 
• Laboratoire de RMN, ICSN-CNRS, 1 ave de la terrasse, 91190 Gif-sur-Yvette, France.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.39 kDa 
• Atom Count: 491 
• Modeled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(P*GP*GP*CP*GP*GP*UP*UP*GP*CP*AP*GP*GP*UP*CP*UP*GP*CP*AP*CP*CP*GP*CP*C)-3'	A	23	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-13 
Deposition Author(s): Fourmy, D., Guittet, E., Yoshizawa, S.

Revision History  

• Version 1.0: 2002-11-13
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-22
  Changes: Data collection