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Cited by 179RNA and protein synthesis mechanismsEnzyme Structure and FunctionRNA modifications and cancer

Importance of potassium ions for ribosome structure and function revealed by long-wavelength X-ray diffraction

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Rozov, Alexey, Khusainov, Iskander, El Omari, Kamel, Duman, Ramona, Mykhaylyk, Vitaliy, Yusupov, Marat, Westhof, Eric, Wagner, Armin +1 more·2019·Nature Communications
DOI 10.1038/s41467-019-10409-4PMC PMC6555806
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Abstract

The ribosome, the largest RNA-containing macromolecular machinery in cells, requires metal ions not only to maintain its three-dimensional fold but also to perform protein synthesis. Despite the vast biochemical data regarding the importance of metal ions for efficient protein synthesis and the increasing number of ribosome structures solved by X-ray crystallography or cryo-electron microscopy, the assignment of metal ions within the ribosome remains elusive due to methodological limitations. Here we present extensive experimental data on the potassium composition and environment in two structures of functional ribosome complexes obtained by measurement of the potassium anomalous signal at the K-edge, derived from long-wavelength X-ray diffraction data. We elucidate the role of potassium ions in protein synthesis at the three-dimensional level, most notably, in the environment of the ribosome functional decoding and peptidyl transferase centers. Our data expand the fundamental knowledge of the mechanism of ribosome function and structural integrity.

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  • Long-wavelength X-ray crystallography suggested a total of ~600 Mg2+ with 334 having inner-sphere coordination and 251 outer sphere coordination.

    “Long-wavelength X-ray crystallography suggested a total of ∼600 Mg2+ with 334 having inner-sphere coordination and 251 outer sphere coordination52 (Figure 4).”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [52]

    The Results (Metal ions assignment; page unavailable) report 334 Mg²⁺ ions and 251 modeled as Mg(H₂O)₆²⁺ in the elongation complex, totaling 585—approximately 600. The paper does not classify those two counts as inner- and outer-sphere coordination, and notes that ions modeled as Mg²⁺ may also be hydrated. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • >3000 cation-binding sites were visualized in the Thermus thermophilus 70S ribosome and assigned as Mg2+, but those assignments have been challenged on experimental and stereochemical grounds.

    “As an upper limit, > 3000 cation-binding sites were visualized in the Thermus thermophilus 70S ribosome51 and assigned as Mg2+, but those assignments have been challenged on both experimental52 and stereochemical54 grounds.”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [52]

  • Stereochemical considerations argue that many sites assigned as Mg2+ in ribosome structures may be occupied instead by K+.

    “Stereochemical considerations argue that many sites assigned as Mg2+ (Figure 4c) may be occupied instead by K+ (Figure 4d).52,54”

    From Metals in Motion: Understanding Labile Metal Pools in Bacteria (2025) · cites this paper as [52]

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Authors
Rozov, A., Khusainov, I., El Omari, K., Duman, R., Mykhaylyk, V., Yusupov, M., Westhof, E., Wagner, A., & Yusupova, G.
Affiliations
  • Centre National de la Recherche Scientifique (FR)
  • Rutherford Appleton Laboratory (GB)
  • Diamond Light Source (GB)
Corresponding author
  • Rozov, Alexey
  • Wagner, Armin
  • Yusupova, Gulnara
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2019-06-07
Volume
10
Issue
1
Pages
2519-2519
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-019-10409-4
PMC
PMC6555806
OpenAlex
W2948631044
Cited by
179
References
1
Citations by year
2026: 21 · 2025: 21 · 2024: 29 · 2023: 20 · 2022: 29 · 2021: 28 · 2020: 23 · 2019: 8
FWCI
7.21
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DORA PSI (Paul Scherrer Institute) (submittedVersion, cc-by)
  • HAL (submittedVersion)
  • HAL Portal Artxiker (Hindustan Aeronautics Limited (India)) (submittedVersion)
  • HAL (submittedVersion, other-oa)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • Agence Nationale de la Recherche (ANR-10-LABX-0030-INRT, ANR-15-CE11-0021-01, ANR-16-CE11-0007-01)
  • Fondation pour la Recherche Médicale (DBF20160635745)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
Keywords
ribosome, potassium ions, metal ions, ribosome structure, protein synthesis, resonant scattering, K-edge, decoding center, peptidyl transferase center
MeSH terms
Cations, Crystallization, Escherichia coli, Potassium, Protein Conformation, Ribosomes, RNA, Transfer, Protein Biosynthesis, X-Ray Diffraction, Thermus thermophilus, Crystallography, X-Ray, Cryoelectron Microscopy

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