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Correction: Consistent global structures of complex RNA states through multidimensional chemical mapping

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Cite as: eLife 2015;4:e10095 doi: 10.7554/eLife.10095

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Cheng CY, Chou FC, Kladwang W, Tian S, Cordero P, Das R. 2015. Consistent global structures of complex RNA states through multidimensional chemical mapping. eLife 4:e07600. doi: 10.7554/eLife.07600

Published 2 June 2015

Table 1 has been corrected. The original manuscript used a previously published formula from Hajdin et al. RNA (2010) for estimating the p-value of a 3D RNA structure prediction but calculated these p-values using the incorrect mean RMSD values. When the correct parameters are used, the p-values of our predictions decrease, i.e. the estimated significances are increased. The conclusions of the manuscript are unchanged.

The corrected table is shown here, with changes highlighted:

Table 1 Corrected. Benchmark of multidimensional chemical mapping on RNAs with crystal structures

RNALengthM2/Rosetta (no MOHCA, control)MCM
RMSD to crystal (Å) (accuracy)p-value§RMSD to crystal (Å) (accuracy)p-value§
Tetrahymena ribozyme P4–P6 domain15838.3>0.98.6<1.0 × 10−16
V. cholerae cyclic-di-GMP riboswitch aptamer, ligand-bound*8911.32.6 × 10−37.66.3 × 10−7
F. nucleatum double glycine riboswitch ligand-binding domain, ligand-bound*15930.5>0.97.9<1.0 × 10−16
S. thermophilum adenosylcobalamin riboswitch aptamer, ligand-bound*16817.1†5.3 × 10−711.94.0 × 10−15
Class I ligase12726.3>0.914.56.8 × 10−5
Class I ligase, core domain‡8714.00.1311.13.1 × 10−3
D. iridis lariat-capping ribozyme1889.6†<1.0 × 10−168.2<1.0 × 10−16
D. iridis lariat-capping ribozyme, MCM refined regions‡6917.0†n.a.§11.2n.a.§

* MCM modeling was performed with MOHCA-seq constraints from datasets collected on the ligand-bound state; ligands were not included during Rosetta modeling.

† M2/Rosetta statistics are reported for RNA-puzzle submission rank 1 models, which included subdomains built by homology modeling.

‡ Calculated over core domain residues or refined regions after alignment using MAMMOTH (Ortiz et al., 2002); see ‘Materials and methods’.

§ p-value computed using analytical formula for secondary-structure-constrained 3D modeling in (Hajdin et al., 2010); it is not applicable to peripheral domains. Value above 0.9 are not well-determined and are presented as > 0.9.

The originally published table is also shown for reference:

Table 1 Original. Benchmark of multidimensional chemical mapping on RNAs with crystal structures

RNALengthM2/RosettaMCM
RMSD to crystal (Å) (accuracy)p-value§RMSD to crystal (Å) (accuracy)p-value§
Tetrahymena ribozyme P4–P6 domain15838.31.08.65.1 × 10−12
V. cholerae cyclic-di-GMP riboswitch aptamer, ligand-bound*8911.30.287.64.3 × 10−3
F. nucleatum double glycine riboswitch ligand-binding domain, ligand-bound*15930.51.07.92.1 × 10−13
S. thermophilum adenosylcobalamin riboswitch aptamer, ligand-bound*16817.1†3.9 × 10−311.91.5 × 10−8
Class I ligase12726.31.014.55.6 × 10−2
Class I ligase, core domain‡8714.00.8611.10.30
D. iridis lariat-capping ribozyme1889.6†1.2 × 10−158.2<1.0 × 10−16
D. iridis lariat-capping ribozyme, MCM refined regions‡6917.0†n.a.§11.2n.a.§

* MCM modeling was performed with MOHCA-seq constraints from datasets collected on the ligand-bound state; ligands were not included during Rosetta modeling.

† M2/Rosetta statistics are reported for RNA-puzzle submission rank 1 models, which included subdomains built by homology modeling.

‡ Calculated over core domain residues or refined regions after alignment using MAMMOTH (Ortiz et al., 2002); see ‘Materials and methods’.

§ p-value computed using analytical formula for secondary-structure-constrained 3D modeling in (Hajdin et al., 2010); it is not applicable to peripheral domains.

Article and author information

Author details

  1. Clarence Yu Cheng

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    The authors declare that no competing interests exist.
  2. Fang-Chieh Chou

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    The authors declare that no competing interests exist.
  3. Wipapat Kladwang

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    The authors declare that no competing interests exist.
  4. Siqi Tian

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    The authors declare that no competing interests exist.
  5. Pablo Cordero

    Competing interests
    The authors declare that no competing interests exist.
  6. Rhiju Das

    Competing interests
    The authors declare that no competing interests exist.

Publication history

  1. Version of Record published: July 21, 2015 (version 1)

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© 2015, Yu Cheng et al.

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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