Huang G, Zhang Y, Zhu X, Zeng C, Wang Q, Zhou Q, Tao Q, Liu M, Lei J, Yan C, Shi Y.

31621092 National Natural Science Foundation of China (National Science Foundation of China), 31430020 National Natural Science Foundation of China (National Science Foundation of China)

	Fig. 1: Cryo-EM structure of a subunit of the cytoplasmic ring (CR) of the Xenopus laevis (X. laevis) NPC. a) The overall EM density map of a CR subunit. The local resolutions between 4.5 Å and 12.5 Å are color-coded. The CR consists of eight subunits. Each subunit is divided into three overlapping regions for soft mask application during data processing: the Core region, the Nup358-containing region, and the Nup214-containing region. These three regions are indicated by dashed boxes. b) The individual EM density maps for the Core, Nup358-containing, and Nup214-containing regions. The local resolutions are color-coded identically as in panel (a). c) The average resolutions for the Core, Nup358-containing, and Nup214-containing regions are 5.5 Å, 7.1 Å and 7.9 Å, respectively. Shown here are the Fourier shell correlation (FSC) plots of the reconstructions for the three regions. The resolutions were estimated on the basis of the FSC value of 0.143. d) Cryo-EM reconstruction of the Core region of the CR subunit. Shown here is the EM density map of the Core region (colored yellow), which is placed in the CR subunit (left panel) and displayed in isolation (right panel). e) Cryo-EM reconstruction of the Nup358-containing region and the Nup214-containing region. Shown here is the EM density map (colored cyan for the Nup358-containing region and green for the Nup214-containing region), which is placed in the CR subunit (left panel) and displayed in isolation (right panel).
	Fig. 2: An atomic model of the CR from the X. laevis NPC. a) Overall structure of the assembled CR at a tilting angle of 45°. Eight copies of the final reconstruction of the CR subunit were docked into the 17.8-Å EM density map of the CR to generate a complete structure (left panel). The coordinates of the X. laevis Y complex were generated through homology modeling and adjusted on the basis of the EM density map. Two copies of the Y complex (colored dark yellow and salmon) were fitted into the density map of each CR subunit. The EM density that cannot be accounted for by the Y complexes is shown and colored yellow (right panel). One CR subunit is boxed. b) A close-up view on the two Y complexes in one CR subunit. Among the two Y complexes, the one located closer to the pore is named the inner Y complex (colored salmon) and the other is termed the outer Y complex (yellow). The EM density yet to be assigned is shown in gray. c) The EM density maps of the Nup358 complex (colored purple), the Nup214 complex (green), and Nup205 (magenta) in each CR subunit. Two views are shown. d) Placement of secondary structural elements in the Nup358 complex (colored cyan), the Nup214 complex (green), and Nup205 (magenta) in each CR subunit. Two views are shown. In addition to the deposited structures of the two Y complexes, the main chains of approximately 5500 amino acids were placed into the EM density maps in our study.
	Fig. 3: Overall organization of the CR. a) Overall structure of the CR. The main-chain model of the CR contains approximately 108,000 amino acids, amounting to a combined molecular mass of nearly 11.9 MDa. Except for two subunits (colored cyan and yellow), subcomplexes in the other six subunits are color-coded. The Y complex, the Nup358 complex, the Nup214 complex, and Nup205 are colored gray, purple blue, green, and magenta, respectively. The 16 Y complexes assemble into a closed ring scaffold, on which the Nup358 complex, the Nup214 complex, and Nup205 associates. b) Close-up views of a CR subunit. Within the same CR subunit, the inner and outer Y complexes associate with each other through two distinct interfaces: one between the inner vertex and outer stem and the other between the inner and outer stems (upper panel). The four Clamps of the Nup358 complex wrap around the stems of the two Y complexes. The two molecules of Nup205 directly interacts with the short and long arms of the two Y complexes (lower panel). The Nup214 complex interacts with the Y complex and Nup205. c) A close-up view of the interface between two neighboring CR subunits. The long arms of the inner and outer Y complexes directly associate with the stems of the inner and outer Y complexes from the neighboring subunit, respectively. In addition, outer Nup205 binds the stem of the inner Y complex from the neighboring subunit.
	Fig. 4: Four Clamps of the Nup358 complex sandwich the stems of the inner and outer Y complexes. a) Domain organization of Nup358 from X. laevis (XlNup358). The various domains are drawn to scale. The thick black lines above the domain organization denote the fragments that have X-ray structures. In particular, the N-terminal domain (NTD, residue 1–145) of human Nup358 contains three TPRs (each encompassing a pair of α-helices). b) The Nup358 complexes associate with the stems of the inner and outer Y complexes. Shown here is a cryo-EM reconstruction of the CR (transparent gray), with the Nup358 complexes shown in purple blue. c) Structural features of the Nup358 complex. The Nup358 complex consists of four Clamps (Clamp-1, -2, -3, and -4, colored purple blue), and a bridge domain (cyan) in the center of the four Clamps. The ω-shaped Clamp-1 contains two U-domains, of which the second (orange) is out of plane with the first U-domain by nearly 90 degrees. The N-terminal 200-residue α-helices of Nup358 were modeled in Clamp-1 and -2. The bridge domain of 23 α-helices closely interacts with Clamp-4. The EM density maps for the N-terminal helices of Clamp-1 and the bridge domain are shown in the lower panels. d) The Nup358 complex clamps the stem of the Y complex. Clamp-1 and Clamp-3 act like a pair of tweezers to hold the stem of the outer Y complex (upper panel). Similarly, Clamp-2 and Clamp-4 constitute a second pair of tweezers to hold the inner Y complex (lower panel). e) The bridge domain of the Nup358 complex directly contacts inner Sec13, inner Nup96, and the finger helix of outer Nup107.
	Fig. 5: Nup205 interacts with the short arm of the Y complex and connects the Y complexes both within the same CR subunit and between adjacent subunits. a) Domain organization of Nup205 and its comparison with Nup188 and Nup192. The domain organization of Nup205 from X. laevis (XlNup205) is displayed along with those of Nup188 from X. laevis (XlNup188) and Nup192 from C. thermophilum (CtNup192) for which the X-ray structure is available. The various domains are drawn to scale. In particular, the C-terminal 250 amino acids of Nup205 (TAIL-C) are predicted to be α-helices but are not represented in the X-ray structure of the CtNup192. b) Nup205 directly interacts with the Y complex. The reconstruction of the CR is displayed in the left panel, with the EM density for Nup205 highlighted in magenta. The EM density maps for the two molecules of Nup205 are shown in the right panel. The Tower helix is clearly identifiable in both maps. c) A close-up view on the locations of the two molecules of Nup205 in each CR subunit. Structures of the two molecules, named inner Nup205 (dark magenta) and outer Nup205 (magenta), are placed in the CR subunit. Proteins in the short arms of the two Y complexes are color-coded. The Nup358 complex is colored light purple blue. All other proteins are colored gray. The EM density map for the Nup214 complex is shown in transparent gray. d) Outer Nup205 closely interacts with the short arm of the outer Y complex and the stem of the inner Y complex from an adjacent CR subunit. The NTD, Tower helix, and TAIL of outer Nup205 associate with the hybrid α-helical domain of outer Nup96N/160C, outer Nup85 and outer Seh1, and outer Nup85, respectively (left panel). The NTD also binds inner Nup43. Outer Nup205 also makes extensive contacts to inner Nup133 and inner Nup107 from the adjacent CR subunit (right panel). e) Inner Nup205 binds the short arm of the inner Y complex (left panel) and the Nup214 complex (right panel). The interactions with the short arm are similar to those by outer Nup205 except that the TAIL of inner Nup205 no longer contacts inner Nup85.
	Fig. 6: The Nup214 complex connects the outer and inner Y complexes. a) Domain organizations of three core components of the Nup214 complex. Nup214, Nup88, and Nup62 from X. laevis (XlNup214, XlNup88 and XlNup62) are thought to constitute the core components of the Nup214 complex; their domain organizations are shown here. Abbreviations: CC, coiled-coil domain; U, unstructured region; FG, Phe-Gly repeats. b) The location of the Nup214 complex in the CR. The overall reconstruction of the CR (colored by transparent gray) is shown, with that of the Nup214 complex colored green. The boxed region of the Nup214 complex is displayed in panels (c) and (d). c) Only a portion of the reconstruction, dubbed “sub-1” for subcomplex-1, displays fine features that allow identification of secondary structural elements. Based on published information, Sub-1 is speculated to consist of a β-propeller from Nup88 and coiled-coil segments (CCS1, CCS2) from Nup214, Nup88 and Nup62. d) The coiled-coil domain of Sub-1 of the Nup214 complex connects the inner and outer Y complexes through direct association with inner and outer Nup85. The EM density for subcomplex-2 (Sub-2) contacts Clamp-4 of the Nup358 complex. The model of Sub-2 is highly speculative and merely shown here for reference (not included in our composite coordinates of the CR). The Nup214 complex projects into the pore of the NPC.
	Fig. S1- Quality analysis of the cryo-EM data for the NPC from X. laevis oocytes. a) Representative data from the tilt-0o series. A representative raw micrograph, the motion trajectory summary, and the CTF distribution are shown in the left, middle, and right panels, respectively. The results of CTF estimation using Gctf1 are shown in the upper right corner of the raw micrograph (left panel). The white circles represent the estimated resolution limit. b) Representative data from the tilt-30o series. c) Representative data from the tilt-45o series. d) Representative data from the tilt-55o series. As the tilting angle increases, the quality of the micrograph gradually decreases. The decrease of quality mainly originates from two aspects. First, particle motion increases as the tilting angle increases (middle panels), because tilting the sample plane projects the doming effect of the Z-direction onto the X-Y plane. Second, sample thickness is inversely proportional to the cosine of the tilting angle, resulting in an increased noise level in the micrograph. Two deliberate measures were taken to alleviate the problem of decreased quality at high tilting angles. First, the total electron dose followed an inverse-cosine scheme to increase contrast at high tilting angles. Second, more micrographs were collected at higher tilting angles. The third but unintentional measure is that a micrograph at a higher tilting angle includes more particles because the view field of on the sample plane is inversely proportional to the cosine of the tilting angle.
	Fig. S2- Structural comparison of the CR from representative studies. a) Our preliminary 18.3-Ã… reconstruction of the CR using single particle analysis. From top to bottom, the four panels display features of the overall CR (colored marine), Nup205 or Nup188 (magenta), the Nup214 complex (green) and the Nup358 complex (purple). b) Cryo-ET structure of the X. laevis NPC using sub-tomogram averaging (STA) (EMD 3005-3008)1. c) Cryo-ET structure of the Homo sapiens (H. sapiens) NPC using STA (EMD-3103)2. Although the EM map of human NPC was used as the initial reference, our reconstruction more closely resembles the cryo-ET reconstruction of the X. laevis NPC in terms of both overall shape and fine features. In particular, the Nup214 complex resembles the cryo-ET X. laevis NPC more than the cryo-ET human NPC. Therefore, our reconstruction was not biased by the initial reference used. Subsequent analysis at the CR subunit level shows a plethora of structural details that were previously unrecognized in low-resolution reconstructions.
	Fig. S3- Cryo-EM data processing. a) A flowchart diagram of preliminary cryo-EM data processing. Only 17,796 particles from 860 movie stacks were used. Details of the data processing are described in the MATERIALS AND METHODS. b) A flowchart diagram of the complete cryo-EM data processing. The CR subunit is divided into three overlapping regions: the Core region, the Nup358-containing region, and the Nup214-containing region. The final reconstructions of the Core region, the Nup358-containing region, and the Nup214- containing region display average resolutions of 5.5 Ã…, 7.1 Ã… and 7.9 Ã…, respectively.
	Fig. S4- The quality of cryo-EM reconstruction for the CR subunit. a) The quality of cryo-EM reconstruction for the Core region. The EM density, angular distribution of the particles used for the final reconstruction, and directional FSC of the Core region are shown in the left, middle, and right panels, respectively. In the angular distribution plot, each cylinder represents one view and the height of the cylinder is proportional to the number of particles for that view. b) The quality of cryo-EM reconstruction for the Nup358-containing region. c) The quality of cryo-EM reconstruction for the Nup214-containing region. All directional FSC curves were prepared using the following website: https://3dfsc.salk.edu1. d) Comparison of our cryo-EM reconstruction of the X. laevis CR with that of the H. sapiens CR2. The same regions of the reconstruction are shown for the cryo-EM reconstruction of the X. laevis CR (upper panels) and the cryo-ET reconstruction of the H. sapiens CR2 (lower panels).
	Fig. S5- Representative EM density maps for Nup85, Seh1 and Nup43 of the Core domain. a) The overall EM density map of Nup85 and Seh1. The EM density maps for Nup85 and Seh1 from the inner and outer Y complexes are shown in the left and right panels, respectively. b) Representative EM density maps for a number of discrete α-helices from inner Nup85. The EM density maps for four pairs of HEAT repeats are shown in the upper panels. c) The EM density maps for the β-propeller domains of inner Seh1 (left panel) and inner and outer Nup43 (right panels). One blade in the Seh1 β-propeller comes from Nup85. All EM density maps in this figure were prepared using the masked Core region map with a contour level between 15σ and 25σ.
	Fig. S6- Representative EM density maps for Nup96N/160C and Sec13 of the Core domain. a) The EM density map of Nup96N/160C. The EM density maps for the NTD of Nup96 and the CTD of Nup160 are shown in the upper panels. Representative EM density maps are shown in the lower panels for selected α-helices of the inner and outer Nup96N/160C. b) The EM density maps of the β-propeller domains in the inner (left panel) and outer (right panel) Sec13. Each β-propeller only has six blades. The unoccupied density for one blade in both cases comes from Nup96. All EM density maps in this figure were prepared using the masked Core region map with a contour level between 15σ and 25σ.
	Fig. S7- The EM density maps for the Nup358 complex. a) The EM density maps for the bridge domain (left panel) and selected α- helices from the bridge domain (right panel). b) Representative EM density maps for selected regions of the Nup358 complex. Shown here are the EM maps for the N- terminal helices of Clamp-1 and Clamp-2 and the U-domain from Clamp-1. All EM density maps in this figure were prepared using the masked Nup358-containing region map with a contour level between 15σ and 25σ.
	Fig. S8- The EM density maps for Nup205. a) The overall EM density maps for the outer and inner Nup205. b) The EM density maps for the MID domain of outer Nup205, which contains a characteristic Tower helix. The ARM repeat and HEAT repeat exhibit contrasting features for their EM density. c) Representative EM density maps for a number of discrete α-helices of outer Nup205. All EM density maps in this figure were prepared using the masked Core region map with a contour level between 15σ and 25σ.
	Fig. S9- The EM density maps for representative interfaces in the CR subunit. a) Representative EM density maps for proteins that interact with Nup205. Shown here are the local EM density maps for the proteins that interact with the NTD (left panel), the Tower helix (middle panel) and TAIL (right panel) of outer Nup205. The individual protein components and their associated density maps are color-coded. b) The EM density maps surrounding the N-terminal domain of outer Nup96. All EM density maps in this figure were prepared using the masked Core region map with a contour level between 15σ and 25σ.
	Fig. S10- Interactions among the Y complexes. a) The final coordinates of the inner and outer Y complexes are placed into the EM density map. Two views are shown. b) Interactions among the Y complexes within the same CR subunit and between two adjacent subunits. The inner and outer Y complexes interact with each other within the same subunit. A pair of Y complex from one subunit associate with its counterpart from the adjacent subunit in a head-to-tail fashion. c) A close-up view on the interface between the inner and outer Y complexes within the same subunit. d) A close-up view on the interface between two neighboring CR subunits. Five areas of interactions are indicated by dashed oval circles.
	Fig. S11- Structural comparison among the Y complexes. a) Structural comparison between the inner and outer Y complexes within the same CR subunit. Two perpendicular views are shown. The inner and outer Y complexes are colored salmon and yellow, respectively. b) Structural comparison between the X. laevis Y complex and the H. sapiens Y complex. Coordinates of the inner and outer Y complexes from X. laevis are superimposed with those from H. sapiens. The overall conformation and main features of the Y complexes remain very similar between these two species. The only notable difference is that the top and bottom faces of the Nup43 β-propeller in the X. laevis Y complexes are opposite of those in the human Y complexes. c) Structural comparison between the X. laevis Y complex with the Myceliophthora thermophila (M. thermophila) Y complex. d) Structural comparison between the X. laevis Y complex with the Saccharomyces cerevisiae (S. cerevisiae) Y complex. The overall conformation of the X. laevis Y complex is similar to that of the S. cerevisiae Y complex, but numerous local structural variations are present. There are no S. cerevisiae homologues for the X. laevis Nup43 and Nup37.
	Fig. S12- The basis for the assignment of Nup205. a) The overall EM density map is more consistent with that for Nup205. The presence of continuous EM density for additional α-helices beyond the predicted C-terminal end of Nup188 favors the assignment of Nup205. Additionally, the length of the EM density for the Tower helix is consistent with that of CtNup192 or X. laevis Nup205. b) Comparison of the Tower helices between X. laevis Nup205 and CtNup192. Inner and outer Nup205 is compared to CtNup192 in the left and right panels, respectively. c) The length of the predicted Tower helix in Nup205 is similar to that of CtNup192 (PDB code: 5HB4). Shown here is a sequence alignment of the Tower helix region between CtNup192 and Nup205 of three vertebrate species. d) The EM density that is connected to the rest of the EM density for Nup205 or Nup188. Seven α- helices (two of them are longer than the other five and are slightly bent in the middle) can be accommodated by the EM density map. Based on the location and continuity of the EM density, these seven α-helices are assigned to the C-terminus of Nup205 (TAIL-C).

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