PDBsum entry 3jro

Transport protein, structural protein

PDB id: 3jro

Contents

Protein chains

701 a.a. *

379 a.a. *

* Residue conservation analysis

PDB id:

3jro

Name:

Transport protein, structural protein

Title:

Nup84-nup145c-sec13 edge element of the npc lattice

Structure:

Fusion protein of protein transport protein sec13 and nucleoporin nup145. Chain: a. Engineered: yes. Nucleoporin nup84. Chain: c. Synonym: nuclear pore protein nup84. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: nup84, ydl116w.

Resolution:

4.00Å R-factor: 0.286 R-free: 0.329

Authors:

S.G.Brohawn,T.U.Schwartz

Key ref:

S.G.Brohawn and T.U.Schwartz (2009). Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice. Nat Struct Biol, 16, 1173-1177. PubMed id: 19855394 DOI: 10.1038/nsmb.1713

Date:

08-Sep-09 Release date: 27-Oct-09

Protein chain

P49687  (NU145_YEAST) -  Nucleoporin NUP145 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1317 a.a.

Struc: 701 a.a.*

Protein chain

Q04491  (SEC13_YEAST) -  Protein transport protein SEC13 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 297 a.a.

Struc: 701 a.a.*

Protein chain

P52891  (NUP84_YEAST) -  Nucleoporin NUP84 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 726 a.a.

Struc: 379 a.a.

* PDB and UniProt seqs differ at 272 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: E.C.3.4.21.- - ?????

DOI no: 10.1038/nsmb.1713

Nat Struct Biol 16:1173-1177 (2009)

PubMed id: 19855394

Molecular architecture of the Nup84-Nup145C-Sec13 edge element in the nuclear pore complex lattice.

S.G.Brohawn, T.U.Schwartz.

ABSTRACT

Nuclear pore complexes (NPCs) facilitate all nucleocytoplasmic transport. These massive protein assemblies are modular, with a stable structural scaffold supporting more dynamically attached components. The scaffold is made from multiple copies of the heptameric Y complex and the heteromeric Nic96 complex. We previously showed that members of these core subcomplexes specifically share an ACE1 fold with Sec31 of the COPII vesicle coat, and we proposed a lattice model for the NPC based on this commonality. Here we present the crystal structure of the heterotrimeric 134-kDa complex of Nup84-Nup145C-Sec13 of the Y complex. The heterotypic ACE1 interaction of Nup84 and Nup145C is analogous to the homotypic ACE1 interaction of Sec31 that forms COPII lattice edge elements and is inconsistent with the alternative 'fence-like' NPC model. We construct a molecular model of the Y complex and compare the architectural principles of COPII and NPC lattices.

Selected figure(s)

Figure 2.
(a) ACE1 crown-crown interaction between Nup145C and Nup84. (b) The same interaction between two Sec31 molecules (PDB 2PM6; ref. 36). The Sec31 interaction is shown without domain swapping, and the rest of the molecules are removed for clarity (see Results). Analogous juxtaposition of crown helices 6, 7 and 8 is observed in both a and b.

Figure 4.
A composite atomic model for the Y complex of the NPC, emphasizing the role of the Nup84–Nup145C edge element as a membrane curvature–stabilizing unit analogous to the Sec31–Sec31 edge element in COPII vesicle coats. The long arm of the Y complex is a composite model from crystal structures and is shown with Nup145C in blue, Sec13 in orange, Nup84 in green and Nup133 in yellow. The relative position of the N-terminal propeller of Nup133 (yellow) and the short arm components Nup120 (blue) and Nup85–Seh1 (blue–orange) are more tentatively placed and shown half-transparent (see Results for details). The long axis of the Y complex is oriented along the positively curved nuclear envelope membrane, with the concave face of the Nup84–Nup145C edge element facing the lipid bilayer. This orientation is analogous to that of the Sec31–Sec31 edge element in the COPII coat and is consistent with the evolutionary relationship between the NPC and COPII vesicle coat lattices. Notably, although the Y complex is shown facing the membrane, it is not predicted to directly contact the nuclear envelope. Rather, other nucleoporins are predicted to have roles that correspond to adaptor complexes in other vesicle coating systems that link the membrane curvature–stabilizing coat (the Y complex) to the nuclear envelope.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 1173-1177) copyright 2009.

Figures were selected by an automated process.