Evidence map›Paper›PMID 21624375›Full record

ArticleJournal of molecular biology2011

Structure of the BamC two-domain protein obtained by Rosetta with a limited NMR data set.

Lisa R Warner, Krisztina Varga, Oliver F Lange, Susan L Baker, David Baker, Marcelo C Sousa, Arthur Pardi

Abstract read
In one paragraph

Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.

0numbers the graph read from it
0cells of the map it votes in
32citing papers in PubMed
–field-weighted citation impact
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

32 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. Article
  5. Review
  6. The big BAM theory: An open and closed case?Biochimica et biophysica acta. Biomembranes · 2020
    Review
  7. Article
  8. Article
  9. Transmembrane β-barrels: Evolution, folding and energetics.Biochimica et biophysica acta. Biomembranes · 2017
    Review
  10. Review
  11. The β-barrel assembly machinery in motion.Nature reviews. Microbiology · 2017
    Review
  12. Article
  13. Article
  14. Article
  15. Review
  16. Article
  17. Article
  18. Article
  19. Article
  20. 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.

Lisa R WarnerDepartment of Chemistry and Biochemistry, University of Colorado, Boulder, Boulder, CO 80309, USA.
Krisztina Varga
Oliver F Lange
Susan L Baker
David Baker
Marcelo C Sousa
Arthur Pardi

Funding

Purchase of 900 MHz NMR SpectrometerP41GM068928 · NIGMS · UNIVERSITY OF COLORADO AT BOULDER · PI WUTTKE, DEBORAH S. · 2003 to 2009
$6.4M
TRAINING IN SIGNAL TRANSDUCTION &CELL CYCLE REGULATIONT32GM008759 · NIGMS · UNIVERSITY OF COLORADO AT BOULDER · PI AHN, NATALIE G. · 2000 to 2020
$5.9M
Predoctoral Training Program in Signaling and Cellular Regulation INCLUDE Down Syndrome SupplementT32GM142607 · NIGMS · UNIVERSITY OF COLORADO · PI Sabrina Leigh Spencer, Tin Tin Su · 2021 to 2026
$3.6M
Transport and Insertion of Outer Membrane ProteinsR01AI080709 · NIAID · UNIVERSITY OF COLORADO · PI SOUSA, MARCELO C. · 2009 to 2016
$2.6M
High resolution structure modeling with RosettaR01GM092802 · NIGMS · UNIVERSITY OF WASHINGTON · PI BAKER, DAVID · 2010 to 2017
$2.3M
Purchase of 800 MHz NMR SpectrometerS10RR016649 · NCRR · UNIVERSITY OF COLORADO AT BOULDER · PI PARDI, ARTHUR · 2002 to 2002
$500k
PURCHASE OF 600 MHZ NMR AND UPGRADE OF NMR FACILITIESS10RR011969 · NCRR · UNIVERSITY OF COLORADO AT BOULDER · PI PARDI, ARTHUR · 1997 to 1997
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NCRR NIH HHS RR16649NCRR NIH HHS S10 RR011969NCRR NIH HHS S10 RR016649NIAID NIH HHS AI080709NIAID NIH HHS R01 AI080709NIGMS NIH HHS GM068928NIGMS NIH HHS GM092802NIGMS NIH HHS P41 GM068928NIGMS NIH HHS R01 GM092802NIGMS NIH HHS T32 GM008759NIGMS NIH HHS T32 GM08759NIGMS NIH HHS T32 GM142607
6 · The paper itself

Abstract

The CS-RDC-NOE Rosetta program was used to generate the solution structure of a 27-kDa fragment of the Escherichia coli BamC protein from a limited set of NMR data. The BamC protein is a component of the essential five-protein β-barrel assembly machine in E. coli. The first 100 residues in BamC were disordered in solution. The Rosetta calculations showed that BamC₁₀₁₋₃₄₄ forms two well-defined domains connected by an ~18-residue linker, where the relative orientation of the domains was not defined. Both domains adopt a helix-grip fold previously observed in the Bet v 1 superfamily. ¹⁵N relaxation data indicated a high degree of conformational flexibility for the linker connecting the N-terminal domain and the C-terminal domain in BamC. The results here show that CS-RDC-NOE Rosetta is robust and has a high tolerance for misassigned nuclear Overhauser effect restraints, greatly simplifying NMR structure determinations.

Indexed as

Computational BiologyEscherichia coliEscherichia coli ProteinsLipid-Linked ProteinsMagnetic Resonance SpectroscopyModels, MolecularProtein FoldingSoftwareBamC protein, E coliEscherichia coli ProteinsLipid-Linked Proteins

Identifiers

PMID21624375
PMCPMC3182476

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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.