PDBsum entry 2raj

Structural protein

PDB id: 2raj

Contents

Protein chain

382 a.a. *

Ligands

SO4

Waters ×13

* Residue conservation analysis

PDB id:

2raj

Name:

Structural protein

Title:

So4 bound px-bar membrane remodeling unit of sorting nexin 9

Structure:

Sorting nexin-9. Chain: a. Fragment: c-terminal fragment, residues 214-594. Synonym: sh3 and px domain-containing protein 1. Protein sdp1. Sh3 and px domain-containing protein 3a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: snx9, sh3px1, sh3pxd3a. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.45Å R-factor: 0.241 R-free: 0.276

Authors:

O.Pylypenko,R.Lundmark,E.Rasmuson,S.R.Carlsson,A.Rak

Key ref:

O.Pylypenko et al. (2007). The PX-BAR membrane-remodeling unit of sorting nexin 9. EMBO J, 26, 4788-4800. PubMed id: 17948057 DOI: 10.1038/sj.emboj.7601889

Date:

16-Sep-07 Release date: 11-Dec-07

Protein chain

Q9Y5X1  (SNX9_HUMAN) -  Sorting nexin-9 from Homo sapiens

Seq: 595 a.a.

Struc: 382 a.a.

DOI no: 10.1038/sj.emboj.7601889

EMBO J 26:4788-4800 (2007)

PubMed id: 17948057

The PX-BAR membrane-remodeling unit of sorting nexin 9.

O.Pylypenko, R.Lundmark, E.Rasmuson, S.R.Carlsson, A.Rak.

ABSTRACT

Sorting nexins (SNXs) form a family of proteins known to interact with components in the endosomal system and to regulate various steps of vesicle transport. Sorting nexin 9 (SNX9) is involved in the late stages of clathrin-mediated endocytosis in non-neuronal cells, where together with the GTPase dynamin, it participates in the formation and scission of the vesicle neck. We report here crystal structures of the functional membrane-remodeling unit of SNX9 and show that it efficiently tubulates lipid membranes in vivo and in vitro. Elucidation of the protein superdomain structure, together with mutational analysis and biochemical and cell biological experiments, demonstrated how the SNX9 PX and BAR domains work in concert in targeting and tubulation of phosphoinositide-containing membranes. The study provides insights into the SNX9-induced membrane modulation mechanism.

Selected figure(s)

Figure 2.
Figure 2 (A) Side view of the SNX9 PX-BAR dimer structure ribbon diagram. BAR domains are shown in red, PX in blue, and the novel Yoke (Y) subdomain in yellow. N- and C-termini are labeled. (B) Top view of the SNX9 PX-BAR dimer structure. The domains are labeled. (C) Ribbon representation of SNX9 Yoke (Y) subdomain structure. The Yoke domain consists of two parts: Y[N] derived from amino-acid residues 214–250 and Y[C] from 375–390. Secondary structure elements are labeled. (D) Sequence alignment of human SNX9 (Q9Y5X1), SNX18 (AAH67860), and SNX30 (ABN09670) PX-BAR domains. The proteins represent a subfamily of PX-BAR SNXs. Secondary structure elements corresponding to the SNX9 structure are monitored. Coloring corresponds to that from panels A–C. Helices are labeled with H, -strands with S, and P denotes a proline-rich motif. The amino-acid residues involved in the dimerization are labeled (+, hydrophobic bar–bar contacts; ^*, H-bond bar–bar contacts), as well as residues involved in interdomain interaction (§, hydrophobic bar-px:y contacts; &, H-bonds bar-px:y contacts). Symbols of consensus sequence are: 2, E/Q; 3, T/S; 4, K/R; 5, Y/F; and 6, hydrophobic.

Figure 3.
Figure 3 (A) SNX9 BAR domain monomer in rainbow colors from the N-terminus in blue to C-terminus in red. -helices are labeled. (B) SNX9 BAR domain. The core and arm regions are monitored, and the proline amino-acid residues at the -helices kinks are labeled.

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 4788-4800) copyright 2007.

Figures were selected by the author.