PDBsum entry 3dyt

Transport protein

PDB id: 3dyt

Contents

Protein chain

355 a.a. *

Ligands

SO4

Waters ×143

* Residue conservation analysis

PDB id:

3dyt

Name:

Transport protein

Title:

Crystal structure of snx9px-bar (230-595), c2221

Structure:

Sorting nexin-9. Chain: a. Fragment: unp residues 230-595. Synonym: sh3 and px domain-containing protein 1, protein sdp1, sh3 and px domain-containing protein 3a. Engineered: yes

Source:

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

Resolution:

2.08Å R-factor: 0.219 R-free: 0.245

Authors:

Q.Wang,H.Y.K.Kaan,H.Sondermann

Key ref:

Q.Wang et al. (2008). Structure and plasticity of Endophilin and Sorting Nexin 9. Structure, 16, 1574-1587. PubMed id: 18940612 DOI: 10.1016/j.str.2008.07.016

Date:

28-Jul-08 Release date: 16-Sep-08

Protein chain

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

Seq: 595 a.a.

Struc: 355 a.a.

DOI no: 10.1016/j.str.2008.07.016

Structure 16:1574-1587 (2008)

PubMed id: 18940612

Structure and plasticity of Endophilin and Sorting Nexin 9.

Q.Wang, H.Y.Kaan, R.N.Hooda, S.L.Goh, H.Sondermann.

ABSTRACT

Endophilin and Sorting Nexin 9 (Snx9) play key roles in endocytosis by membrane curvature sensing and remodeling via their Bin/Amphiphysin/Rvs (BAR) domains. BAR and the related F-BAR domains form dimeric, crescent-shaped units that occur N- or C-terminally to other lipid-binding, adaptor, or catalytic modules. In crystal structures, the PX-BAR unit of Snx9 (Snx9(PX-BAR)) adopts an overall compact, moderately curved conformation. SAXS-based solution studies revealed an alternative, more curved state of Snx9(PX-BAR) in which the PX domains are flexibly connected to the BAR domains, providing a model for how Snx9 exhibits lipid-dependent curvature preferences. In contrast, Endophilin appears to be rigid in solution, and the SH3 domains are located at the distal tips of a BAR domain dimer with fixed curvature. We also observed tip-to-tip interactions between the BAR domains in a trigonal crystal form of Snx9(PX-BAR) reminiscent of functionally important interactions described for F-BAR domains.

Selected figure(s)

Figure 1.
Figure 1. Structural Comparison of BAR Domain and BAR Domain-Related Proteins
(A–F) Crystal structures of (A) Snx9^PX-BAR (Pylypenko et al., 2007; this study) and of the (B) BAR-PH module of APPL1 (PDB: 2ELB) ([Li et al., 2007] and [Zhu et al., 2007]) are shown in two orthogonal views in their dimeric state. Dimeric crystal structures of isolated N-BAR domains from (C) Endophilin (PDB: 1X03) (Masuda et al., 2006) and (D) Amphiphysin (PDB: 1URU) (Peter et al., 2004), the (E) F-BAR domain from CIP4 (PDB: 3EFK) (Shimada et al., 2007), and the (F) I-BAR domain of IRSp53 (PDB: 1Y2O) (Millard et al., 2005) are shown. The degree of curvature of BAR domain dimers is indicated as gray lines.

Figure 2.
Figure 2. Structure of Snx9^PX-BAR
(A) Domain organization of Sorting Nexin 9 (Snx9) and Endophilin. Schematic presentations and binding partners of the domains in Endophilin and Snx9 are shown.
(B) Crystal structure of Snx9^PX-BAR. Two orthogonal views of Snx9^PX-BAR (residues 230–595 of human Snx9; space group C222[1]) are shown; the PX domains are green and brown, and the BAR domains are orange and gray. The membrane interaction surface is indicated as a dashed line.
(C) Local differences in the structures of Snx9. The structure of Snx9^PX-BAR (residues 230–595) was superimposed onto Snx9^PX-BAR, including the N-terminal amphipathic helix and helix α1Y[N] of the yoke domain (residues 214–595; PDB: 2RAJ) (Pylypenko et al., 2007).

The above figures are reprinted by permission from Cell Press: Structure (2008, 16, 1574-1587) copyright 2008.

Figures were selected by the author.