5IZK

The crystal structure of human eEFSec in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.298 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation.

Dobosz-Bartoszek, M.Pinkerton, M.H.Otwinowski, Z.Chakravarthy, S.Soll, D.Copeland, P.R.Simonovic, M.

(2016) Nat Commun 7: 12941-12941

  • DOI: https://doi.org/10.1038/ncomms12941
  • Primary Citation of Related Structures:  
    5IZK, 5IZL, 5IZM

  • PubMed Abstract: 

    Selenocysteine is the only proteinogenic amino acid encoded by a recoded in-frame UGA codon that does not operate as the canonical opal stop codon. A specialized translation elongation factor, eEFSec in eukaryotes and SelB in prokaryotes, promotes selenocysteine incorporation into selenoproteins by a still poorly understood mechanism. Our structural and biochemical results reveal that four domains of human eEFSec fold into a chalice-like structure that has similar binding affinities for GDP, GTP and other guanine nucleotides. Surprisingly, unlike in eEF1A and EF-Tu, the guanine nucleotide exchange does not cause a major conformational change in domain 1 of eEFSec, but instead induces a swing of domain 4. We propose that eEFSec employs a non-canonical mechanism involving the distinct C-terminal domain 4 for the release of the selenocysteinyl-tRNA during decoding on the ribosome.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Selenocysteine-specific elongation factor
A, B
616Homo sapiensMutation(s): 0 
Gene Names: EEFSECSELB
UniProt & NIH Common Fund Data Resources
Find proteins for P57772 (Homo sapiens)
Explore P57772 
Go to UniProtKB:  P57772
PHAROS:  P57772
GTEx:  ENSG00000132394 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP57772
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.338 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.298 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.691α = 90
b = 96.861β = 90.25
c = 125.408γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM097042
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM070773
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM22854

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description