Huang G et al. (2022), Cryo-EM structure of the nuclear ring from Xeno...

XB-ART-58964

Cell Res 2022 Apr 01;324:349-358. doi: 10.1038/s41422-021-00610-w.

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Cryo-EM structure of the nuclear ring from Xenopus laevis nuclear pore complex.

Huang G , Zhan X , Zeng C , Zhu X , Liang K , Zhao Y , Wang P , Wang Q , Zhou Q , Tao Q , Liu M , Lei J , Yan C .

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Nuclear pore complex (NPC) shuttles cargo across the nuclear envelope. Here we present single-particle cryo-EM structure of the nuclear ring (NR) subunit from Xenopus laevis NPC at an average resolution of 5.6 Å. The NR subunit comprises two 10-membered Y complexes, each with the nucleoporin ELYS closely associating with Nup160 and Nup37 of the long arm. Unlike the cytoplasmic ring (CR) or inner ring (IR), the NR subunit contains only one molecule each of Nup205 and Nup93. Nup205 binds both arms of the Y complexes and interacts with the stem of inner Y complex from the neighboring subunit. Nup93 connects the stems of inner and outer Y complexes within the same NR subunit, and places its N-terminal extended helix into the axial groove of Nup205 from the neighboring subunit. Together with other structural information, we have generated a composite atomic model of the central ring scaffold that includes the NR, IR, and CR. The IR is connected to the two outer rings mainly through Nup155. This model facilitates functional understanding of vertebrate NPC.

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Species referenced: Xenopus laevis
Genes referenced: ahctf1 nup155 nup160 nup205 nup37 nup93

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	Fig. 1. Cryo-EM structure of the NR subunit of the X. laevis NPC.a A cartoon diagram of the central ring scaffolds of the NPC. The central ring scaffolds consist of the CR, IR, and NR. Cytoplasmic filaments and nuclear basket are connected to the CR and NR, respectively. Two views are shown to highlight the NR (colored cyan). b Cryo-EM reconstruction of the NR subunit at an average resolution of 5.6 Å. The Fourier Shell Correlation (FSC) over resolution and distribution of local resolution for the EM reconstruction are shown in the left and right panels, respectively. c Structure of the NR subunit from X. laevis NPC. Two related views are shown. Individual nucleoporins are shown in surface representation (left panel) and as color-coded cartoon (right panel). The structurally resolved NR subunit contains 22 molecules of 12 distinct nucleoporins, one molecule each for Nup205/Nup93 and two molecules each for the other 10 nucleoporins. The latter 20 nucleoporins constitute two Y complexes. Compared to the CR subunit, each Y complex in the NR subunit associates with one molecule of ELYS. Nup155 comes from the IR subunit. d Structure comparison between the NR and CR subunits from X. laevis NPC. Two molecules of ELYS are uniquely present in the NR subunit, but not the CR subunit. The two Y complexes of the NR subunit can be superimposed with those of the CR subunit with an RMSD of ~8.2 Å over 11,517 aligned Cα atoms. e Structure of the CR subunit from X. laevis NPC. The nucleoporins that are absent in the NR subunit are color-coded: five molecules of Nup358 (green), inner Nup205 (marine), an additional molecule of Nup93 (red), and Nup88 (orange) of the Nup214 complex.
	Fig. 2. Association of ELYS with the long arm of the Y complex in X. laevis NR.a The N-terminal domain of ELYS associates with the long arm of the Y complex in the NR subunit. The outer ELYS (marine) and inner ELYS (purple) associate with the outer and inner Y complexes, respectively. b Structure of the long arm of the inner Y complex. The long arm, spanning a length of ~23 nm, consists of Nup160, Nup37, and ELYS. Inner ELYS from one NR subunit also associates with inner Nup133 from an adjacent subunit. c A close-up view on the interface between the two N-terminal β-propellers of inner ELYS and inner Nup160. d A close-up view on the interface between the α-solenoid of ELYS and Nup37. e A close-up view on the extended interface between the α-helical domain of Nup160 and ELYS. In short, eight helices and three loops from inner ELYS engage in interactions with structural elements from inner Nup160, including seven helices from the inner Nup160 α-helical domain. f A close-up view on the interactions of the C-terminal α-helices of inner ELYS with the C-terminal α-helices of inner Nup85, inner Nup96, and inner Nup160. g A close-up view on the interface between the α-helical domain of inner ELYS and the α-helical domain of inner Nup133 from the adjacent subunit. Helix α10 of inner ELYS closely interacts with the loop between α5 and α6 of inner Nup133. All loops involved in the interaction between nucleoporins are highlighted in thicker form.
	Fig. 3. Nup205 connects the inner and outer Y complexes in the NR subunit.a Nup205 connects the inner and outer Y complexes. Nup205 interacts with the short arm and the vertex of outer Y complex; it also associates with both arms of inner Y complex. b A close-up view on the association between Nup205 and inner Y complex. The association involves inner Nup37 from the long arm and inner Nup43 from the short arm. c A close-up view on the interface between the N-terminal domain of Nup205 and the vertex region of outer Y complex. d A close-up view on the interface between the C-terminal domain of Nup205 and outer Nup85. e Structure alignment of Nup205 and its binding partners from the NR subunit with those from the CR subunit.
	Fig. 4. Nup93 bridges the stems of inner and outer Y complexes in the NR subunit.a Nup93 bridges the stems of inner and outer Y complexes. The NR subunit contains one molecule each of Nup93 and Nup205. The extended N-terminal helix from Nup93 in subunit 1 (S1) may interact with Nup205 in the neighboring subunit (S2). b A close-up view on the interface between Nup93 and Nup205. Helix α5 of Nup93 traverses through the axial groove of the Nup205 α-solenoid. c Two close-up views on the interface between Nup93 and the vertex of inner Y complex. d A close-up view on the interface between the CTD of Nup93 and the stem of outer Y complex. e Structure alignment of Nup205 between the NR and IR subunits. Helix α5 of Nup93 remains bound to Nup205 in both cases. These two structures can be superimposed with an RMSD of ~2.8 Å over 1517 aligned Cα atoms. f Structure alignment of Nup93 and its binding partners from the NR subunit with those from the CR subunit. This alignment produces an RMSD of ~2.9 Å over 1818 aligned Cα atoms.
	Fig. 5. Formation of the NR scaffold.a A composite model of the X. laevis NR. The X. laevis NR has inner and outer diameters of ~75 nm and ~130 nm, respectively. Two neighboring subunits, subunit 1 (S1) and subunit 2 (S2), are labeled by text with S2 highlighted in a dashed box. b A close-up view of the boxed region in a, showing the clustered interfaces between S1 and S2. The nucleoporins from S1 and S2 are shown as color-coded cartoon and surface representation, respectively. c A close-up view on the inter-subunit interface mediated by Nup205 from one subunit (S2) and Nup93 and inner Nup107 from the adjacent subunit (S1). d A close-up view on the inter-subunit interface mediated by three nucleoporins (Nup205, outer Nup85 and outer Nup160) from S2 and inner Nup107 and inner Nup133 from S1. e A close-up view on the inter-subunit interface mediated by the long arms of the Y complexes from S2 and the stem tips of the Y complexes from S1.
	Fig. 6. Structure of the central ring scaffold of X. laevis NPC.a Overall structure of the central ring scaffold (CR/IR/NR) of X. laevis NPC. Combining the atomic models of the CR24 and IR,25 we generated a composite model of the central ring scaffold of X. laevis NPC. Shown here are two perpendicular views. All nucleoporins are color-coded and tabulated below the images. The X. laevis NPC has outer and inner diameters of ~130 nm and ~45 nm, respectively. b Overall structure of one subunit of the central ring scaffold. Two perpendicular views are shown, with nucleoporins color-coded. The CR and NR subunits are placed symmetrically on the cytoplasmic and nuclear sides, respectively, of the symmetric IR subunit. The subunit is anchored on the NE mainly through NDC1 and the β-propeller domains from Nup155, Nup160, Nup133 and ELYS. The CR and NR are linked to the IR mainly through two molecules of Nup155. c A close-up view on the interface between the linker Nup155 and CR components. The C-terminal helices of linker Nup155 are sandwiched by inner Nup160 and inner Nup205 from the CR subunit. d A close-up view on the interface between linker Nup155 and NR components. The C-terminal helices of linker Nup155 contact the middle portion of the α-helical domain of inner Nup160 from the NR.

References [+] :

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