5ELQ

Crystal structure of the SNX27 PDZ domain bound to the C-terminal DGKzeta PDZ binding motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A molecular code for endosomal recycling of phosphorylated cargos by the SNX27-retromer complex.

Clairfeuille, T.Mas, C.Chan, A.S.Yang, Z.Tello-Lafoz, M.Chandra, M.Widagdo, J.Kerr, M.C.Paul, B.Merida, I.Teasdale, R.D.Pavlos, N.J.Anggono, V.Collins, B.M.

(2016) Nat.Struct.Mol.Biol. 23: 921-932

  • DOI: 10.1038/nsmb.3290
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Recycling of internalized receptors from endosomal compartments is essential for the receptors' cell-surface homeostasis. Sorting nexin 27 (SNX27) cooperates with the retromer complex in the recycling of proteins containing type I PSD95-Dlg-ZO1 (PDZ) ...

    Recycling of internalized receptors from endosomal compartments is essential for the receptors' cell-surface homeostasis. Sorting nexin 27 (SNX27) cooperates with the retromer complex in the recycling of proteins containing type I PSD95-Dlg-ZO1 (PDZ)-binding motifs. Here we define specific acidic amino acid sequences upstream of the PDZ-binding motif required for high-affinity engagement of the human SNX27 PDZ domain. However, a subset of SNX27 ligands, such as the β2 adrenergic receptor and N-methyl-D-aspartate (NMDA) receptor, lack these sequence determinants. Instead, we identified conserved sites of phosphorylation that substitute for acidic residues and dramatically enhance SNX27 interactions. This newly identified mechanism suggests a likely regulatory switch for PDZ interaction and protein transport by the SNX27-retromer complex. Defining this SNX27 binding code allowed us to classify more than 400 potential SNX27 ligands with broad functional implications in signal transduction, neuronal plasticity and metabolite transport.


    Organizational Affiliation

    Institute for Molecular Bioscience, University of Queensland, St. Lucia, Queensland, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sorting nexin-27
A, B
101Rattus norvegicusMutation(s): 0 
Gene Names: Snx27 (Mrt1)
Find proteins for Q8K4V4 (Rattus norvegicus)
Go to UniProtKB:  Q8K4V4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLU-ASP-GLN-GLU-THR-ALA-VAL
P, C
8Homo sapiensMutation(s): 0 
Gene Names: DGKZ (DAGK6)
EC: 2.7.1.107
Find proteins for Q13574 (Homo sapiens)
Go to Gene View: DGKZ
Go to UniProtKB:  Q13574
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, B, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.940α = 90.00
b = 54.120β = 90.00
c = 74.240γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)AustraliaAPP1058734

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Database references
  • Version 1.2: 2016-10-19
    Type: Database references
  • Version 1.3: 2017-09-27
    Type: Author supporting evidence, Data collection, Derived calculations