2UWM

C-TERMINAL DOMAIN(WH2-WH4) OF ELONGATION FACTOR SELB IN COMPLEX WITH SECIS RNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

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This is version 1.1 of the entry. See complete history. 


Literature

Structural Basis for Dynamic Interdomain Movement and RNA Recognition of the Selenocysteine-Specific Elongation Factor Selb.

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

(2007) Structure 15: 577

  • DOI: 10.1016/j.str.2007.03.007
  • Primary Citation of Related Structures:  
    2UWM

  • PubMed Abstract: 

    • Selenocysteine (Sec) is the "21st" amino acid and is genetically encoded by an unusual incorporation system. The stop codon UGA becomes a Sec codon when the selenocysteine insertion sequence (SECIS) exists downstream of UGA. Sec incorporation requires a specific elongation factor, SelB, which recognizes tRNA(Sec) via use of an EF-Tu-like domain and the SECIS mRNA hairpin via use of a C-terminal domain (SelB-C) ...

    Selenocysteine (Sec) is the "21st" amino acid and is genetically encoded by an unusual incorporation system. The stop codon UGA becomes a Sec codon when the selenocysteine insertion sequence (SECIS) exists downstream of UGA. Sec incorporation requires a specific elongation factor, SelB, which recognizes tRNA(Sec) via use of an EF-Tu-like domain and the SECIS mRNA hairpin via use of a C-terminal domain (SelB-C). SelB functions in multiple translational steps: binding to SECIS mRNA and tRNA(Sec), delivery of tRNA(Sec) onto an A site, GTP hydrolysis, and release from tRNA and mRNA. However, this dynamic mechanism remains to be revealed. Here, we report a large domain rearrangement in the structure of SelB-C complexed with RNA. Surprisingly, the interdomain region forms new interactions with the phosphate backbone of a neighboring RNA, distinct from SECIS RNA binding. This SelB-RNA interaction is sequence independent, possibly reflecting SelB-tRNA/-rRNA recognitions. Based on these data, the dynamic SelB-ribosome-mRNA-tRNA interactions will be discussed.

    Organizational Affiliation: 

    Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SELENOCYSTEINE-SPECIFIC ELONGATION FACTORA, B258Moorella thermoaceticaMutation(s): 0 
UniProt
Find proteins for Q2RFK4 (Moorella thermoacetica (strain ATCC 39073 / JCM 9320))
Explore Q2RFK4 
Go to UniProtKB:  Q2RFK4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2RFK4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-R(*GP*GP*CP*GP*UP*UP*GP*CP*CP*GP *GP*UP*CP*UP*GP*GP*CP*AP*AP*CP*GP*CP*C)-3'C, D 23Moorella thermoacetica
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.074α = 90
b = 119.843β = 100.05
c = 50.461γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance