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Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles

Cell Research volume 33, pages 867–878 (2023)Cite this article

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Abstract

Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo continuous maturation steps in the nucleoplasm, and prepare for nuclear export. Here, we report eleven cryo-EM structures of the nuclear pre-60S particles isolated from human cells through epitope-tagged GNL2, at resolutions of 2.8–4.3 Å. These high-resolution snapshots provide fine details for several major structural remodeling events at a virtual temporal resolution. Two new human nuclear factors, L10K and C11orf98, were also identified. Comparative structural analyses reveal that many assembly factors act as successive place holders to control the timing of factor association/dissociation events. They display multi-phasic binding properties for different domains and generate complex binding inter-dependencies as a means to guide the rRNA maturation process towards its mature conformation. Overall, our data reveal that nuclear assembly of human pre-60S particles is generally hierarchical with short branch pathways, and a few factors display specific roles as rRNA chaperones by confining rRNA helices locally to facilitate their folding, such as the C-terminal domain of SDAD1.

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Fig. 1: Cryo-EM structures of human pre-60S particles obtained through epitope-tagged GNL2.
Fig. 2: Continuous conformational maturation of the CP in GNL2-particles.
Fig. 3: The C-terminal region of SDAD1 functions in chaperoning the folding of H80.
Fig. 4: Structure and interaction of human L10K in state F.
Fig. 5: Structure of the human ITS2-associated factors.
Fig. 6: Structural dynamics and interactional changes of GNL2 in GNL2-particles.

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Data availability

The cryo-EM maps and atomic coordinates of the states A, B’, C’, C, D’, D, E, F’, F, G’ and G have been deposited in the EMDB and PDB databases with accession codes EMD-35672, EMD-35673, EMD-35649, EMD-35639, EMD-35651, EMD-35599, EMD-35375, EMD-35597, EMD-35371, EMD-35596, EMD-35370 and PDB 8IR1, 8IR3, 8IPX, 8IPD, 8IPY, 8INK, 8IE3, 8INF, 8IDY, 8INE, 8IDT, respectively.

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Acknowledgements

We thank Drs. W. Wei, X. Ji and J. Hu at Peking University for their help with CRISPR Knock-In experiments. We also thank the Core Facilities at the School of Life Sciences, Peking University for help with negative staining EM; the Cryo-EM Platform of Peking University for help with data collection; the High-performance Computing Platform of Peking University for help with computation; the National Center for Protein Sciences at Peking University for assistance with flow cytometry and mass spectrometry. The work was supported by the National Natural Science Foundation of China (32230051 to N.G., 31922036 to N.L.), the National Key R&D Program of China (2019YFA0508904 to N.G.), and the Qidong-SLS Innovation Fund to N.G.

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  1. State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China

    Yunyang Zhang, Xiaomeng Liang, Sha Luo, Yan Chen, Yu Li, Chengying Ma, Ningning Li & Ning Gao

  2. Changping Laboratory, Beijing, China

    Chengying Ma, Ningning Li & Ning Gao

  3. National Biomedical Imaging Center, Peking University, Beijing, China

    Ning Gao

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Contributions

Y.Z. and S.L. established the CRISPR-KI cell line. Y.Z. prepared the pre-ribosomal samples, and collected the cryo-EM data. Y.Z. and X.L. performed EM analysis (with the help of Y.L., Y.C., N.L. and C.M.). N.G., Y.Z. and X.L. performed cryo-EM model building and wrote the manuscript.

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Correspondence to Ning Gao.

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Zhang, Y., Liang, X., Luo, S. et al. Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles. Cell Res 33, 867–878 (2023). https://doi.org/10.1038/s41422-023-00853-9

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