PDBsum entry 3f7f

Structural protein

PDB id: 3f7f

Contents

Protein chains

701 a.a. *

Metals

_HG ×12

* Residue conservation analysis

PDB id:

3f7f

Name:

Structural protein

Title:

Structure of nup120

Structure:

Nucleoporin nup120. Chain: a, b, c, d. Fragment: unp residues 1-729. Synonym: nuclear pore protein nup120. Engineered: yes. Mutation: yes

Source:

Saccharomyces cerevisiae. Organism_taxid: 4932. Gene: nup120, rat2, ykl057c, ykl314, ykl313. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.232 R-free: 0.254

Authors:

H.S.Seo,Y.Ma,E.W.Debler,G.Blobel,A.Hoelz

Key ref:

H.S.Seo et al. (2009). Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex. Proc Natl Acad Sci U S A, 106, 14281-14286. PubMed id: 19706512 DOI: 10.1073/pnas.0907453106

Date:

08-Nov-08 Release date: 18-Aug-09

Protein chains

P35729  (NU120_YEAST) -  Nucleoporin NUP120 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1037 a.a.

Struc: 701 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1073/pnas.0907453106

Proc Natl Acad Sci U S A 106:14281-14286 (2009)

PubMed id: 19706512

Structural and functional analysis of Nup120 suggests ring formation of the Nup84 complex.

H.S.Seo, Y.Ma, E.W.Debler, D.Wacker, S.Kutik, G.Blobel, A.Hoelz.

ABSTRACT

The Nup84 complex constitutes a key building block in the nuclear pore complex (NPC). Here we present the crystal structure of one of its 7 components, Nup120, which reveals a beta propeller and an alpha-helical domain representing a novel fold. We discovered a previously unidentified interaction of Nup120 with Nup133 and confirmed the physiological relevance in vivo. As mapping of the individual components in the Nup84 complex places Nup120 and Nup133 at opposite ends of the heptamer, our findings indicate a head-to-tail arrangement of elongated Nup84 complexes into a ring structure, consistent with a fence-like coat for the nuclear pore membrane. The attachment site for Nup133 lies at the very end of an extended unstructured region, which allows for flexibility in the diameter of the Nup84 complex ring. These results illuminate important roles of terminal unstructured segments in nucleoporins for the architecture, function, and assembly of the NPC.

Selected figure(s)

Figure 2.
Structural analysis of the Nup120 NTD domains. (A) Ribbon representation of the Nup120 β propeller domain. The 7 blades of the β propeller core (yellow), the location of the disordered 1E1A loop (orange), the 3D4A loop (red), the α-helical insertion in the 6D7A loop (blue), and their secondary structure elements are indicated. (B) Schematic representation of the Nup120 β propeller domain and the locations of its various insertions. (C) Ribbon representation of the Nup120 α-helical domain. The leucine zipper–like core (orange) and the 9 surrounding α-helices (green) are indicated. A 180°-rotated view is shown on the right.

Figure 5.
Model for the ring formation of the Nup84 complex. (A) Schematic representation of the heptameric complex and the approximate localization of its 7 nups (19). (B) The interaction of Nup120 and Nup133 suggests the intermolecular interaction between 2 heptamers in a head-to-tail fashion mediated by a short stretch at the very N terminus of an extended unstructured region of Nup133. (C) Eight heptamers are arranged in a closed ring with a diameter of ≈1,000 Å in accordance with the NPC dimensions determined by cryo-electron microscopy (8).

Figures were selected by an automated process.