1LVA

Crystal structure of a C-terminal fragment of Moorella thermoacetica elongation factor SelB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB.

Selmer, M.Su, X.D.

(2002) EMBO J 21: 4145-4153

  • DOI: 10.1093/emboj/cdf408
  • Primary Citation of Related Structures:  
    1LVA

  • PubMed Abstract: 
  • SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu) ...

    SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). We present the crystal structure of a C-terminal fragment of SelB (SelB-C) from Moorella thermoacetica at 2.12 A resolution, solved by a combination of selenium and yttrium multiwavelength anomalous dispersion. This 264 amino acid fragment contains the entire C-terminal extension beginning after the EF-Tu-homologous domains. SelB-C consists of four similar winged-helix domains arranged into the shape of an L. This is the first example of winged-helix domains involved in RNA binding. The location of conserved basic amino acids, together with data from the literature, define the position of the mRNA-binding site. Steric requirements indicate that a conformational change may occur upon ribosome interaction. Structural observations and data in the literature suggest that this change happens upon mRNA binding.


    Related Citations: 
    • Preparation of a crystallizable mRNA-binding fragment of Moorella thermoacetica elongation factor SelB
      Selmer, M., Wilting, R., Holmlund, D., Su, X.-D.
      (2002) Acta Crystallogr D Biol Crystallogr 58: 1871

    Organizational Affiliation

    Department of Molecular Biophysics, Lund University, PO Box 124, S-221 00 Lund, Sweden. maria@mrc-lmb.cam.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Selenocysteine-specific elongation factorA258Moorella thermoaceticaMutation(s): 1 
Gene Names: SelB(amino acids 370-634)selB
UniProt
Find proteins for Q46455 (Moorella thermoacetica)
Explore Q46455 
Go to UniProtKB:  Q46455
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46455
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Y1
Query on Y1

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
YTTRIUM ION
Y
KAJPZYFHSCFBCI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.841α = 90
b = 67.006β = 90
c = 105.357γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2002-05-28 
  • Released Date: 2002-08-21 
  • Deposition Author(s): Selmer, M., Su, X.-D.

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-21
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance