Evidence map›Paper›PMID 27708257›Full record

ArticleNature communications2016

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

Malgorzata Dobosz-Bartoszek, Mark H Pinkerton, Zbyszek Otwinowski, Srinivas Chakravarthy, Dieter Söll, Paul R Copeland, Miljan Simonović

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
18citing papers in PubMed, 1 pooled it
2.1field-weighted citation impact, top 13% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

18 citing papers in PubMed, 1 synthesis or guideline pooled it, 35 citations in OpenAlex.

  1. Pooled it
  2. Article
  3. Article
  4. Article
  5. Article
  6. Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Article
  13. Article
  14. Ribosome Fate during Decoding of UGA-Sec Codons.International journal of molecular sciences · 2021
    Review
  15. Article
  16. HOxidative medicine and cellular longevity · 2019
    Article
  17. Review
  18. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors at 5 institutions in 1 country.

Malgorzata Dobosz-BartoszekDepartment of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
Mark H PinkertonDepartment of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.
Zbyszek OtwinowskiDepartment of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.
Srinivas ChakravarthyBiophysics Collaborative Access Team/Illinois Institute of Technology, Sector 18ID, Advanced Photon Source, Chicago, Illinois 60439, USA.
Dieter SöllDepartments of Molecular Biophysics and Biochemistry, and Chemistry, Yale University, New Haven, Connecticut 06520, USA.
Paul R CopelandDepartment of Biochemistry and Molecular Biology, Rutgers-Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.
Miljan SimonovićDepartment of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois 60607, USA.
Rutgers, The State University of New Jersey · USUniversity of Illinois Chicago · USIllinois Institute of Technology · USThe University of Texas Southwestern Medical Center · USYale University · US

Funding

Yale Clinical and Translational Science Award (U Component)UL1TR001863 · NCATS · YALE UNIVERSITY · PI John H. Krystal, LUCILA OHNO-MACHADO · 2016 to 2026
$102.9M
TRANSFER RNAR01GM022854 · NIGMS · YALE UNIVERSITY · PI SOLL, DIETER · 1985 to 2016
$21.3M
Time resolved SAXS studies on the RP2/Arl3 complex pp.484-485P41GM103622 · NIGMS · ILLINOIS INSTITUTE OF TECHNOLOGY · PI IRVING, THOMAS C · 2012 to 2020
$11.9M
X-RAY CRYSTALLOGRAPHY OF MACROMOLECULESR01GM053163 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI MINOR, WLADEK, OTWINOWSKI, ZBYSZEK · 1996 to 2014
$6.3M
Functional Analysis of SBP2 and Selenocysteine IncorporationR01GM077073 · NIGMS · UNIV OF MED/DENT NJ-R W JOHNSON MED SCH · PI COPELAND, PAUL R · 2006 to 2022
$5.5M
The mechanism of selenium incorporation into selenocysteine in humans.R01GM097042 · NIGMS · UNIVERSITY OF ILLINOIS AT CHICAGO · PI POLIKANOV, YURY · 2012 to 2021
$3.0M
The Midwest Center for Structural Genomics - Community ResourceR24GM115586 · NIGMS · UNIVERSITY OF CHICAGO · PI JOACHIMIAK, ANDRZEJ · 2015 to 2017
$2.8M
Mechanisms of CIC Chloride Transport ProteinsR01GM070773 · NIGMS · STANFORD UNIVERSITY · PI MADUKE, MERRITT C · 2005 to 2009
$1.5M
X-ray data analysis in the presence of structural variability - Administrative SupplementR01GM117080 · NIGMS · UT SOUTHWESTERN MEDICAL CENTER · PI MINOR, WLADEK, OTWINOWSKI, ZBYSZEK · 2015 to 2018
$1.4M
TRANSFER RNAR37GM022854 · NIGMS · YALE UNIVERSITY · PI SOLL, DIETER G · 1991 to 2000
$786k
Advanced Pixel Array Detector for Time-Resolved SAXS and Fiber DiffractionS10OD018090 · OD · ILLINOIS INSTITUTE OF TECHNOLOGY · PI IRVING, THOMAS C · 2014 to 2014
$529k
NCATS NIH HHS UL1 TR001863NIGMS NIH HHS P41 GM103622NIGMS NIH HHS R01 GM022854NIGMS NIH HHS R01 GM053163NIGMS NIH HHS R01 GM070773NIGMS NIH HHS R01 GM077073NIGMS NIH HHS R01 GM097042NIGMS NIH HHS R01 GM117080NIGMS NIH HHS R24 GM115586NIGMS NIH HHS R37 GM022854NIH HHS S10 OD018090
6 · The paper itself

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.

Indexed as

Codon, TerminatorCrystallography, X-RayGuanosine DiphosphateGuanosine TriphosphateHumansPeptide Elongation FactorsPhylogenyProtein BiosynthesisProtein DomainsProtein Structure, SecondaryRibosomesRNA, Transfer, Amino AcylSelenocysteineSelenoproteinsCodon, TerminatorEEFSEC protein, humanGuanosine DiphosphateGuanosine TriphosphatePeptide Elongation FactorsRNA, Transfer, Amino AcylSelenocysteineselenocysteinyl-tRNASelenoproteins

Identifiers

PMID27708257
PMCPMC5059743
OpenAlexW2529529221

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.