1LVA

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

• PDB DOI: https://doi.org/10.2210/pdb1LVA/pdb

• Classification: TRANSLATION
• Organism(s): Moorella thermoacetica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.258 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.203 (DCC) 

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

• PubMed: 12145214 
• DOI: https://doi.org/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). 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.

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Organizational Affiliation: 

Department of Molecular Biophysics, Lund University, PO Box 124, S-221 00 Lund, Sweden. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.01 kDa 
• Atom Count: 2,190 
• Modelled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Selenocysteine-specific elongation factor	A	258	Moorella thermoacetica	Mutation(s): 1  Gene Names: SelB(amino acids 370-634)
UniProt
Find proteins for Q46455 (Moorella thermoacetica) Explore Q46455  Go to UniProtKB:  Q46455

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
Y1	B [auth A], C [auth A]	YTTRIUM ION Y KAJPZYFHSCFBCI-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.258 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.203 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.841	α = 90
b = 67.006	β = 90
c = 105.357	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• 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
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary