Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
Cited by 362

The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.

Visualization of chemical modifications in the human 80S ribosome structure

Open access
Natchiar, S. Kundhavai, Myasnikov, Alexander G., Kratzat, Hanna, Hazemann, Isabelle, Klaholz, Bruno P.·2017·Nature
DOI 10.1038/nature24482
Open this paper in CoChat — free account

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/nature24482

Cites

7 of 7 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 7 references

Research works printed but not linked: 64

  1. Rodnina, M. V., Fischer, N., Maracci, C. & Stark, H. Ribosome dynamics during decoding. Phil. Trans. R. Soc. Lond. B 372, 1716 (2017) · DOI
  2. Decatur, W. A. & Fournier, M. J. rRNA modifications and ribosome function. Trends Biochem. Sci. 27, 344–351 (2002) · DOI · Paper page
  3. Cantara, W. A. et al. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res. 39, D195–D201 (2011) · DOI · Paper page
  4. Machnicka, M. A. et al. MODOMICS: a database of RNA modification pathways—2013 update. Nucleic Acids Res. 41, D262–D267 (2013) · DOI · Paper page
  5. Sharma, S. & Lafontaine, D. L. J. ‘View from a bridge’: a new perspective on eukaryotic rRNA base modification. Trends Biochem. Sci. 40, 560–575 (2015) · DOI
  6. Maden, B. E. Identification of the locations of the methyl groups in 18 S ribosomal RNA from Xenopus laevis and man. J. Mol. Biol. 189, 681–699 (1986) · DOI
  7. Maden, B. E. Locations of methyl groups in 28 S rRNA of Xenopus laevis and man: clustering in the conserved core of molecule. J. Mol. Biol. 201, 289–314 (1988) · DOI
  8. Piekna-Przybylska, D., Decatur, W. A. & Fournier, M. J. The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Nucleic Acids Res. 36, D178–D183 (2008) · DOI
  9. Baxter-Roshek, J. L., Petrov, A. N. & Dinman, J. D. Optimization of ribosome structure and function by rRNA base modification. PLoS One 2, e174 (2007) · DOI
  10. Ofengand, J. & Bakin, A. Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J. Mol. Biol. 266, 246–268 (1997) · DOI
  11. Green, R. & Noller, H. F. In vitro complementation analysis localizes 23S rRNA posttranscriptional modifications that are required for Escherichia coli 50S ribosomal subunit assembly and function. RNA 2, 1011–1021 (1996)
  12. Auffinger, P. & Westhof, E. in Effects of Pseudouridylation on tRNA Hydration and Dynamics: A Theoretical Approach in Modification and Editing of RNA (eds Grosjean, H. & Benne, R. ) 103–112 (ASM, 1998) · DOI
  13. Long, K. S. & Vester, B. Resistance to linezolid caused by modifications at its binding site on the ribosome. Antimicrob. Agents Chemother. 56, 603–612 (2012) · DOI · Paper page
  14. Benítez-Páez, A., Cárdenas-Brito, S., Corredor, M., Villarroya, M. & Armengod, M. E. Impairing methylations at ribosome RNA, a point mutation-dependent strategy for aminoglycoside resistance: the rsmG case. Biomedica 34 (Suppl. 1), 41–49 (2014) · DOI
  15. Stojković, V., Noda-Garcia, L., Tawfik, D. S. & Fujimori, D. G. Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme. Nucleic Acids Res. 44, 8897–8907 (2016) · DOI
  16. Wirmer, J. & Westhof, E. Molecular contacts between antibiotics and the 30S ribosomal particle. Methods Enzymol. 415, 180–202 (2006) · DOI
  17. Gonzales, B. et al. The Treacher Collins syndrome (TCOF1) gene product is involved in pre-rRNA methylation. Hum. Mol. Genet. 14, 2035–2043 (2005) · DOI
  18. Freed, E. F., Bleichert, F., Dutca, L. M. & Baserga, S. J. When ribosomes go bad: diseases of ribosome biogenesis. Mol. Biosyst. 6, 481–493 (2010) · DOI
  19. Penzo, M., Galbiati, A., Treré, D. & Montanaro, L. The importance of being (slightly) modified: the role of rRNA editing on gene expression control and its connections with cancer. Biochim. Biophys. Acta 1866, 330–338 (2016)
  20. Lafontaine, D. L. J. Noncoding RNAs in eukaryotic ribosome biogenesis and function. Nat. Struct. Mol. Biol. 22, 11–19 (2015) · DOI · Paper page
  21. Bellodi, C. et al. H/ACA small RNA dysfunctions in disease reveal key roles for noncoding RNA modifications in hematopoietic stem cell differentiation. Cell Reports 3, 1493–1502 (2013) · DOI
  22. Khatter, H., Myasnikov, A. G., Natchiar, S. K. & Klaholz, B. P. Structure of the human 80S ribosome. Nature 520, 640–645 (2015) · DOI · Paper page
  23. Myasnikov, A. G. et al. Structure–function insights reveal the human ribosome as a cancer target for antibiotics. Nat. Commun. 7, 12856 (2016) · DOI
  24. Fischer, N. et al. Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM. Nature 520, 567–570 (2015) · DOI · Paper page
  25. Polikanov, Y. S., Melnikov, S. V., Söll, D. & Steitz, T. A. Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat. Struct. Mol. Biol. 22, 342–344 (2015) · DOI · Paper page
  26. Shalev-Benami, M. et al. 2.8-Å cryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania. Cell Reports 16, 288–294 (2016) · DOI
  27. von Loeffelholz, O. et al. Focused classification and refinement in high-resolution cryo-EM structural analysis of ribosome complexes. Curr. Opin. Struct. Biol. 46, 140–148 (2017) · DOI
  28. Voorhees, R. M., Fernández, I. S., Scheres, S. H. W. & Hegde, R. S. Structure of the mammalian ribosome–Sec61 complex to 3.4 Å resolution. Cell 157, 1632–1643 (2014) · DOI · Paper page
  29. Limbach, P. A., Crain, P. F. & McCloskey, J. A. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 22, 2183–2196 (1994) · DOI · Paper page
  30. Zorbas, C. et al. The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis. Mol. Biol. Cell 26, 2080–2095 (2015) · DOI
  31. Baudin-Baillieu, A. et al. Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy. Nucleic Acids Res. 37, 7665–7677 (2009) · DOI
  32. Liang, X.-H., Liu, Q. & Fournier, M. J. Loss of rRNA modifications in the decoding center of the ribosome impairs translation and strongly delays pre-rRNA processing. RNA 15, 1716–1728 (2009) · DOI
  33. Meyer, B. et al. Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans. Nucleic Acids Res. 44, 4304–4316 (2016) · DOI
  34. Ito, S. et al. A single acetylation of 18 S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae. J. Biol. Chem. 289, 26201–26212 (2014) · DOI
  35. Sharma, S. et al. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Nucleic Acids Res. 43, 2242–2258 (2015) · DOI · Paper page
  36. Hermann, T. & Westhof, E. Non-Watson–Crick base pairs in RNA–protein recognition. Chem. Biol. 6, R335–R343 (1999) · DOI
  37. Swann, P. F. Why do O6-alkylguanine and O4-alkylthymine miscode? The relationship between the structure of DNA containing O6-alkylguanine and O4-alkylthymine and the mutagenic properties of these bases. Mutat. Res. 233, 81–94 (1990) · DOI
  38. Sergeeva, O. V., Bogdanov, A. A. & Sergiev, P. V. What do we know about ribosomal RNA methylation in Escherichia coli? Biochimie 117, 110–118 (2015) · DOI
  39. Hudson, B. H. & Zaher, H. S. O6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity. RNA 21, 1648–1659 (2015) · DOI
  40. Herzig, M. C. S. et al. DNA alkylating agent protects against spontaneous hepatocellular carcinoma regardless of O6-methylguanine-DNA methyltransferase status. Cancer Prev. Res. (Phila.) 9, 245–252 (2016) · DOI
  41. Marcel, V . et al. p53 acts as a safeguard of translational control by regulating fibrillarin and rRNA methylation in cancer. Cancer Cell 24, 318–330 (2013) · DOI · Paper page
  42. Farley, K. I. & Baserga, S. J. Probing the mechanisms underlying human diseases in making ribosomes. Biochem. Soc. Trans. 44, 1035–1044 (2016) · DOI
  43. Dinman, J. D. Pathways to specialized ribosomes: the Brussels lecture. J. Mol. Biol. 428 (10 Pt B), 2186–2194 (2016) · DOI
  44. Slavov, N., Semrau, S., Airoldi, E., Budnik, B. & van Oudenaarden, A. Differential stoichiometry among core ribosomal proteins. Cell Reports 13, 865–873 (2015) · DOI
  45. Preiss, T. All ribosomes are created equal. Really? Trends Biochem. Sci. 41, 121–123 (2016) · DOI
  46. Marcel, V., Catez, F. & Diaz, J.-J. Ribosome heterogeneity in tumorigenesis: the rRNA point of view. Mol. Cell. Oncol. 2, e983755 (2015) · DOI
  47. Krogh, N. et al. Profiling of 2′-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic Acids Res. 44, 7884–7895 (2016) · DOI · Paper page
  48. Khatter, H. et al. Purification, characterization and crystallization of the human 80S ribosome. Nucleic Acids Res. 42, e49 (2014) · DOI
  49. Garreau de Loubresse, N. et al. Structural basis for the inhibition of the eukaryotic ribosome. Nature 513, 517–522 (2014) · DOI · Paper page
  50. Borovinskaya, M. A., Shoji, S., Fredrick, K. & Cate, J. H. D. Structural basis for hygromycin B inhibition of protein biosynthesis. RNA 14, 1590–1599 (2008) · DOI
  51. Gürel, G., Blaha, G., Moore, P. B. & Steitz, T. A. U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome. J. Mol. Biol. 389, 146–156 (2009) · DOI
  52. Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017) · DOI · Paper page
  53. Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016) · DOI
  54. Chen, S. et al. High-resolution noise substitution to measure overfitting and validate resolution in 3D structure determination by single particle electron cryomicroscopy. Ultramicroscopy 135, 24–35 (2013) · DOI · Paper page
  55. Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014) · DOI · Paper page
  56. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004) · DOI · Paper page
  57. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010) · DOI · Paper page
  58. Natchiar, K. S., Myasnikov, A. G., Kratzat, H., Hazemann, I. & Klaholz, B. P. Atomic model building and refinement into high-resolution cryo-EM maps. Protocol Exchange http://dx.doi.org/10.1038/protex.2017.122 (2017) · DOI
  59. Lebedev, A. A. et al. JLigand: a graphical tool for the CCP4 template-restraint library. Acta Crystallogr. D Biol. Crystallogr. 68, 431–440 (2012) · DOI · Paper page
  60. Yang, H., Henning, D. & Valdez, B. C. Functional interaction between RNA helicase II/Guα and ribosomal protein L4. FEBS J. 272, 3788–3802 (2005) · DOI
  61. Gigova, A., Duggimpudi, S., Pollex, T., Schaefer, M. & Koš, M. A cluster of methylations in the domain IV of 25S rRNA is required for ribosome stability. RNA 20, 1632–1644 (2014) · DOI
  62. Sharma, S., Yang, J., Watzinger, P., Kötter, P. & Entian, K.-D. Yeast Nop2 and Rcm1 methylate C2870 and C2278 of the 25S rRNA, respectively. Nucleic Acids Res. 41, 9062–9076 (2013) · DOI
  63. Schosserer, M. et al. Methylation of ribosomal RNA by NSUN5 is a conserved mechanism modulating organismal lifespan. Nat. Commun. 6, 6158 (2015) · DOI · Paper page
  64. Chow, C. S., Lamichhane, T. N. & Mahto, S. K. Expanding the nucleotide repertoire of the ribosome with post-transcriptional modifications. ACS Chem. Biol. 2, 610–619 (2007) · DOI

Cited by

See all 362

Metadata

Authors
Natchiar, S. K., Myasnikov, A. G., Kratzat, H., Hazemann, I., & Klaholz, B. P.
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2017-11-01
Volume
551
Issue
7681
Pages
472-477
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature24482
OpenAlex
W4256485542
Cited by
362
References
7
FWCI
11.84
Type
journal article
Language
en
Open access
green
Licence

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Visualization of chemical modifications in the human 80S ribosome structure. https://app.cochat.ai/papers/10.1038/nature24482
The paper
Natchiar, S. K., Myasnikov, A. G., Kratzat, H., Hazemann, I., & Klaholz, B. P. (2017). Visualization of chemical modifications in the human 80S ribosome structure. Nature. https://doi.org/10.1038/nature24482

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.