From Beamline X29A: Structural evolution of the membrane-coating module of the nuclear pore complex.

The coatomer module of the nuclear pore complex borders the cylinder-like nuclear pore-membrane domain of the nuclear envelope. In evolution, a single coatomer module increases in size from hetero-heptamer (Saccharomyces cerevisiae) to hetero-octamer (Schizosaccharomyces pombe) to hetero-nonamer (Metazoa). Notably, the heptamer-octamer transition proceeds through the acquisition of the nucleoporin Nup37. How Nup37 contacts the heptamer remained unknown. Using recombinant nucleoporins, we show that Sp-Nup37 specifically binds the Sp-Nup120 member of the hetero-heptamer but does not bind an Sc-Nup120 homolog. To elucidate the Nup37-Nup120 interaction at the atomic level, we carried out crystallographic analyses of Sp-Nup37 alone and in a complex with an N-terminal, ~110-kDa fragment of Sp-Nup120 comprising residues 1-950. Corroborating structural predictions, we determined that Nup37 folds into a seven-bladed .-propeller. Several disordered surface regions of the Nup37 .-propeller assume structure when bound to Sp-Nup120. The N-terminal domain of Sp-Nup120(1-950) also folds into a seven-bladed β propeller with a markedly protruding 6D-7A insert and is followed by a contorted helical domain. Conspicuously, this 6D-7A insert contains an extension of 50 residues which also is highly conserved in Metazoa but is absent in Sc-Nup120. Strikingly, numerous contacts with the Nup37 .-propeller are located on this extension of the 6D-7A insert. Another contact region is situated toward the end of the helical region of Sp-Nup120(1-950). Our findings provide information about the evolution and the assembly of the coatomer module of the nuclear pore complex.

Figure: Bicycle-like structure of the Sp-Nup1201-950Sp-Nup37 complex. (A) Cartoon representation of the nonliganded (Upper) and bound (Lower) forms of Nup37 showing the bottom of the β-propeller. Of the four disordered regions (dotted lines, Upper), three assume structure in the bound form (Lower). (B) Ribbon representation from two angles; blue, β-propeller domain of Nup120; green, 6D-7A insert of β-propeller; wheat, helical domain of Nup120; cyan, β-propeller of Nup37. The blades of the two β-propeller structures (note their opposite orientation) and some prominent α-helices are labeled. Note that the helical domain of Nup120 (wheat) provides much of the bicycle frame including one side of each of the two prongs for mounting the two wheels, with the other side provided by the β-propeller insert (green); the "front" wheel is the Nup120 β-propeller; the "rear" wheel is the Nup37 β-propeller. (C) Schematic tracing of polypeptide chains of Sp-Nup1201-950 and full-length Nup37; α-strands of β-propellers (A-E) are indicated by thick arrows; &alpha-helices (h1-h30) are indicated by rectangles and are numbered in order of their occurrence from the N to the C terminus; loops are indicated by lines, and disordered regions are indicated by dotted lines; a dotted outline indicates a portion of β-propeller insert that is absent in Sc-Nup120.

Results from:
Liu X, Mitchell JM, Wozniak RW, Blobel G, Fan J.
Structural evolution of the membrane-coating module of the nuclear pore complex.
Proc Natl Acad Sci U S A. 2012 Oct 9;109(41):16498-503. doi: 10.1073/pnas.1214557109. Epub 2012 Sep 26.
PMCID: PMC3478598