5EMA

Crystal structure of the SNX27 PDZ domain bound to the phosphorylated C-terminal LRRC3B PDZ binding motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    5EM9, 5ELQ, 5EMB, 5EMA

  • 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 β 2 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sorting nexin-27A101Rattus norvegicusMutation(s): 0 
Gene Names: Snx27Mrt1
Find proteins for Q8K4V4 (Rattus norvegicus)
Explore Q8K4V4 
Go to UniProtKB:  Q8K4V4
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ASP-ASP-ILE-SEP-THR-VAL-VALB8Homo sapiensMutation(s): 0 
Gene Names: LRRC3BLRP15UNQ195/PRO221
Find proteins for Q96PB8 (Homo sapiens)
Explore Q96PB8 
Go to UniProtKB:  Q96PB8
NIH Common Fund Data Resources
PHAROS  Q96PB8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
BL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.171α = 90
b = 48.49β = 90
c = 56.229γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1041929
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1058734

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2016-10-19
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence, Data collection, Derived calculations
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence