In situ architecture of the algal nuclear pore complex

Abstract

Nuclear pore complexes (NPCs) span the nuclear envelope and mediate nucleocytoplasmic exchange. They are a hallmark of eukaryotes and deeply rooted in the evolutionary origin of cellular compartmentalization. NPCs have an elaborate architecture that has been well studied in vertebrates. Whether this architecture is unique or varies significantly in other eukaryotic kingdoms remains unknown, predominantly due to missing in situ structural data. Here, we report the architecture of the algal NPC from the early branching eukaryote Chlamydomonas reinhardtii and compare it to the human NPC. We find that the inner ring of the Chlamydomonas NPC has an unexpectedly large diameter, and the outer rings exhibit an asymmetric oligomeric state that has not been observed or predicted previously. Our study provides evidence that the NPC is subject to substantial structural variation between species. The divergent and conserved features of NPC architecture provide insights into the evolution of the nucleocytoplasmic transport machinery.

Fig. 1

Structure of the CrNPC in comparison to the HsNPC. a Structures are displayed as rendered isosurfaces, sliced through the central axis. Green arrowheads indicate the connector element, which is absent from the cytoplasmic side of the CrNPC. b Cytoplasmic face view. The CrNPC central channel is dilated. c Cytoplasmic and nuclear rings of both NPCs. The CrNPC cytoplasmic ring has reduced density compared to the HsNPC. Black and magenta arrowheads indicate the density attributed to the Nup159 (Nup214 in humans) subcomplex, which forms cytoplasmic filaments that protrude towards the central channel. CR cytoplasmic ring, IR inner ring, and NR nuclear ring

Fig. 2

The inner ring of the CrNPC is dilated compared to the HsNPC. a Structures of the CrNPC and the HsNPC, displayed as rendered isosurfaces, sliced through the central axis. The inner rings (IR) are indicated with dashed boxes (top). The four protomers of the asymmetric unit (orange: outer protomers, blue: inner protomers), each containing Nup93 and Nup62 subcomplexes, explain the inner ring densities of both the CrNPC (bottom left) and HsNPC (bottom right). b View of the CrNPC and HsNPC inner rings seen along the nucleocytoplasmic axis. The asymmetric units (spokes) of the CrNPC inner ring are separated from each other (left), leaving relatively large peripheral channels (arrowheads) between the spokes, whereas the spokes of the HsNPC are positioned closer together (right)

Fig. 3

The CrNPC has 24 Y-complexes. a Segmented Y-complexes according to the fits presented in Supplementary Figs. 6, 8, and 9 are shown superimposed with the inner ring structure (gray). The distribution of Y-complexes in the CrNPC is asymmetric across the nuclear envelope plane. The cytoplasmic ring has only eight Y-complexes (orange), whereas the nuclear ring has 16 (orange and light blue). In the HsNPC, the distribution is symmetric, with 16 Y-complexes in both of the outer rings. b Rotated views of the CrNPC and HsNPC, sliced through the central axis. Density attributed to large scaffold Nups (Nup205/Nup188) in the outer rings of the HsNPC (dark blue) is found between the inner (light blue) and outer (orange) copies of the Y-complexes. Similar density is observed in the CrNPC, although this assignment remains tentative at the given resolution. Enlarged views on the bottom row show the presence of only one connector element (green) in the CrNPC (red box), with the cytoplasmic ring lacking the connector (blue box), while the HsNPC contains two connector elements and duplicated Y-complexes (purple box). CR cytoplasmic ring, IR inner ring, and NR nuclear ring