Structure of a trimeric nucleoporin complex reveals alternate oligomerization states - PubMed (original) (raw)

Structure of a trimeric nucleoporin complex reveals alternate oligomerization states

Vivien Nagy et al. Proc Natl Acad Sci U S A. 2009.

Abstract

The heptameric Nup84 complex constitutes an evolutionarily conserved building block of the nuclear pore complex. Here, we present the crystal structure of the heterotrimeric Sec13 x Nup145C x Nup84 complex, the centerpiece of the heptamer, at 3.2-A resolution. Nup84 forms a U-shaped alpha-helical solenoid domain, topologically similar to two other members of the heptamer, Nup145C and Nup85. The interaction between Nup84 and Nup145C is mediated via a hydrophobic interface located in the kink regions of the two solenoids that is reinforced by additional interactions of two long Nup84 loops. The Nup84 binding site partially overlaps with the homo-dimerization interface of Nup145C, suggesting competing binding events. Fitting of the elongated Z-shaped heterotrimer into electron microscopy (EM) envelopes of the heptamer indicates that structural changes occur at the Nup145C x Nup84 interface. Docking the crystal structures of all heptamer components into the EM envelope constitutes a major advance toward the completion of the structural characterization of the Nup84 complex.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

Structure of the S. cerevisiae Sec13·Nup145C·Nup84 NTD complex. (A) Schematic representation of the heptameric complex and the approximate localization of its seven nups (21). (B) Domain structures of Sec13, Nup145C, and Nup84. For Sec13, the six WD40 repeats (orange) are indicated. For Nup145C, the unstructured N-terminal region (gray), the domain invasion motif (DIM) (green), the αB-αC connector (C) (red), the α-helical domain (blue), and the C-terminal α-helical region (pink) are indicated. For Nup84, the N-terminal domain (NTD) and C-terminal domain (CTD) are indicated. The residue numbering is shown below and the bars above the domain structures mark the crystallized fragments of the three proteins. (C) Structure of Sec13·Nup145C·Nup84 NTD in ribbon representation, colored as in panel B. A 90°-rotated view is shown on the right. (D) Schematic representation of the Sec13·Nup145C·Nup84 NTD heterotrimer.

Fig. 2.

Fig. 2.

The Nup84 α-helical domain. Ribbon representation of the Nup84 NTD is shown in rainbow colors along the polypeptide chain from the N- to the C- terminus. The four loops that participate in the Nup145C·Nup84 interaction are indicated.

Fig. 3.

Fig. 3.

Surface properties of the Nup84 NTD. The surface orientations are identical in all columns. A black line encircles the Nup145C interaction surface. (A) Surface rendition of the Nup84 NTD. The Nup145C contact surface is colored in blue, while the remaining surface is colored in yellow. As a reference, a surface rendition of the heterotrimer is shown to the left, colored according to Fig. 1_C_. (B) Surface representation colored according to a multispecies sequence alignment, ranging from 60% similarity (white) to 100% identity (red) (

Fig. S4

). (C) Surface rendition colored according to the electrostatic potential, ranging from −10 kBT/e (red) to + 10 kBT/e (blue). Note the two conserved hydrophobic patches located toward the periphery of the extended Nup145C-interacting surface.

Fig. 4.

Fig. 4.

Interaction of the Nup84 NTD with the Nup145C solenoid domain. The Sec13·Nup145C·Nup84 NTD heterotrimer is shown in ribbon representation, colored according to Fig. 1_C_. The kink regions of the two solenoids interact in a head-to-head fashion. The Nup84 NTD protrudes with an approximate 40° angle from the Nup145C U-shaped solenoid. The inset marks the Nup145C·Nup84 interface that is illustrated in detail on the right. For clarity, the interface shown on the right is rotated by 90°. For Nup145C, the solenoid subdomain (blue) and helix αE (green) are indicated. For Nup84, the interface helices (yellow), as well as the long αE-αF (red) and αH-αI (magenta) connectors that mediate the interaction with Nup145C are indicated.

Fig. 5.

Fig. 5.

Binding promiscuity of Nup145C. (A) Surface rendition of the Sec13·Nup145C nucleoporin pair derived from the Sec13·Nup145C hetero-octamer (Nup145C·Nup145C homo-dimerization) and the Sec13·Nup145C·Nup84 NTD heterotrimer (Nup145C·Nup84 NTD hetero-dimerization). The Nup145C homo-dimerization and hetero-dimerization surfaces are colored in green and yellow, respectively. The Sec13 and the remaining Nup145C surfaces are colored in orange and blue, respectively. (B) 90°-rotated views of the Sec13·Nup145C pair colored according to panel A (top), to a multispecies sequence alignment, ranging from 60% similarity (white) to 100% identity (red) (26) (middle), and to the electrostatic potential, from −10 kBT/e (red) to +10 kBT/e (blue). The orientation of all surface representations is identical in each column. As a reference, black lines encircle the Nup145C homo-dimerization and Nup84-interaction surfaces.

Fig. 6.

Fig. 6.

Protein arrangement within the heptameric complex. (A) Docking of crystal structures into the EM envelope of the heptameric Nup84 complex. A 90°-rotated view is shown on the right. The approximate 40° angle by which the Nup84 NTD protrudes from the Sec13·Nup145 nucleoporin pair nicely follows one of the two kink regions of the heptamer stem. (B) EM envelope of the second reconstructed conformation of the heptamer in which the two hinge regions are completely extended, forming an almost entirely straight stem. (C) Superposition of the two determined heptamer conformations. The kink region at the Nup145C·Nup84 interface is indicated and was used for the structural alignment, showing that this interface corresponds to a hinge in the heptamer stem.

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References

    1. Reichelt R, et al. Correlation between structure and mass distribution of the nuclear pore complex and of distinct pore complex components. J Cell Biol. 1990;110:883–894. - PMC - PubMed
    1. Pemberton LF, Paschal BM. Mechanisms of receptor-mediated nuclear import and nuclear export. Traffic. 2005;6:187–198. - PubMed
    1. Hoelz A, Blobel G. Cell biology: Popping out of the nucleus. Nature. 2004;432:815–816. - PubMed
    1. Debler EW, Blobel G, Hoelz A. Nuclear transport comes full circle. Nat Struct Mol Biol. 2009;5:457–459. - PubMed
    1. Cook A, Bono F, Jinek M, Conti E. Structural biology of nucleocytoplasmic transport. Annu Rev Biochem. 2007;76:647–671. - PubMed

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