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

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


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: https://doi.org/10.1038/nsmb.3290
  • Primary Citation of Related Structures:  
    5ELQ, 5EM9, 5EMA, 5EMB

  • 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)-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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sorting nexin-27A,
C [auth B]
101Rattus norvegicusMutation(s): 0 
Gene Names: Snx27Mrt1
Find proteins for Q8K4V4 (Rattus norvegicus)
Explore Q8K4V4 
Go to UniProtKB:  Q8K4V4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K4V4
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D [auth C]
8Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13574 (Homo sapiens)
Explore Q13574 
Go to UniProtKB:  Q13574
PHAROS:  Q13574
GTEx:  ENSG00000149091 
Entity Groups  
UniProt GroupQ13574
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.94α = 90
b = 54.12β = 90
c = 74.24γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

  • 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
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description