Westlake News ACADEMICS

Prof. Yigong Shi’s Lab at Westlake University Reports High-resolution cryo-EM Structure of the Cytoplasmic Ring from the Xenopus laevis Nuclear Pore Complex

20, 2022

Email: zhangchi@westlake.edu.cn
Phone: +86-(0)571-86886861
Office of Public Affairs

The nuclear pore complex (NPC) is the only route for bi-directional cargo transport across the nuclear envelope (NE). It is also one of the largest and most complicated molecular machines inside the eukaryotic cell. The NPC plays a vital role in keeping the homeostasis in the nucleus, protecting the genetic materials, and the regulation of gene expression. Its malfunction is related to multiple diseases including cancer. A high-resolution structure of the NPC facilitates understanding of the basic processes of life and the mechanisms underlying diseases, which may further inspire development of related therapies or drugs.

The NPC resides on the NE. From cytoplasm to nucleoplasm, it consists of cytoplasmic filaments (CF), a cytoplasmic ring (CR), an inner ring (IR), a luminal ring (LR), a nuclear ring (NR), and a nuclear basket (NB) (Figure 1). The CR, IR, and NR form the most stable scaffold of the NPC. The CF and NB attach to the CR and NR, respectively. The CF, IR and NB contain nucleoporins that are rich in FG repeats, which form the diffusion barrier of the NPC, which is responsible for transport selectivity. In addition, the NPC displays C8 symmetry along the axis perpendicular to the NE. An NPC contains 500-1000 nucleoporins, and its mass reaches ~60 MDa in yeast, ~110 MDa in humans.

Figure 1  The structure of the NPC

Recently, Prof. Shi’s lab at Westlake University published an article online in Science (https://www.science.org/doi/10.1126/science.abl8280) titled “Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex”. The article reports the single-particle cryo-EM structure of the CR subunit from Xenopus laevis NPC with the highest resolution to date.

This team studies the Xenopus laevis NPC mainly through cryo-EM single particle analysis. The team collected 46,143 micrographs, in which 800,825 NPC particles were manually picked out for data processing. Through multiple iterations of computation, they were finally able to reconstruct the CR subunit of the NPC at 3.7- to 4.7-Å resolution. At the same time, they also solved an amino-terminal domain of Nup358 at 3.0 Å through recombinant expression and cryo-EM single particle analysis. Based on the reconstructions above, the team built the most accurate model of the CR to date (Figure 2).

Figure 2  The cryo-EM structure of the CR subunit

This model of the CR subunit included five Nup358, two Nup205, and two Nup93 molecules in addition to the two previously characterized Y complexes. The carboxyl-terminal fragment of Nup160 served as an organizing center at the vertex of each Y complex. Structural analysis revealed how Nup93, Nup205, and Nup358 facilitate and strengthen the assembly of the CR scaffold that is primarily formed by two layers of Y complexes.

Together with other structural information from Prof. Shi’s lab, the team generated a composite atomic model of the central ring scaffold (Figure 3) that includes the CR, IR, and NR, which is the most detailed and accurate structural model

Figure 3  The Central