1WSU | pdb_00001wsu

C-terminal domain of elongation factor selB complexed with SECIS RNA

• PDB DOI: https://doi.org/10.2210/pdb1WSU/pdb
• NAKB: 1WSU

• Classification: TRANSLATION/RNA
• Organism(s): Neomoorella thermoacetica
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-11-11 Released: 2005-01-25 
• Deposition Author(s): Yoshizawa, S., Rasubala, L., Ose, T., Kohda, D., Fourmy, D., Maenaka, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Structural basis for mRNA recognition by elongation factor SelB

Yoshizawa, S., Rasubala, L., Ose, T., Kohda, D., Fourmy, D., Maenaka, K.

(2005) Nat Struct Mol Biol 12: 198-203

• PubMed: 15665870 
• DOI: https://doi.org/10.1038/nsmb890
• Primary Citation of Related Structures:  
  1WSU


• PubMed Abstract: 
  

  In bacteria, incorporation of selenocysteine, the 21(st) amino acid, into proteins requires elongation factor SelB, which has the unusual property of binding to both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity, the molecular basis of which has been unknown. We have determined the crystal structure of the mRNA-binding domain of SelB in complex with SECIS RNA at a resolution of 2.3 A. This is the first example of a complex between an RNA and a winged-helix (WH) domain, a motif found in many DNA-binding proteins and recently discovered in RNA-binding proteins. Notably, RNA binding does not induce a major conformational change in the WH motif. The structure reveals a new mode of RNA recognition with a geometry that allows the complex to wrap around the small ribosomal subunit.

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Organizational Affiliation: 

Laboratoire de RMN, Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 79.13 kDa 
• Atom Count: 5,484 
• Modeled Residue Count: 534 
• Deposited Residue Count: 565 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Selenocysteine-specific elongation factor	D [auth A], E [auth B], F [auth C], G [auth D]	124	Neomoorella thermoacetica	Mutation(s): 0  Gene Names: selB
UniProt
Find proteins for Q46455 (Moorella thermoacetica) Explore Q46455  Go to UniProtKB:  Q46455

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP*GP*UP*CP*U*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'	A [auth E], B [auth F], C [auth G]	23	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.279 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.865	α = 90
b = 169.814	β = 90
c = 71.827	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-25 
Deposition Author(s): Yoshizawa, S., Rasubala, L., Ose, T., Kohda, D., Fourmy, D., Maenaka, K.

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description