7RM8

Solution NMR structure of PDLIM7 PDZ bound to SNX17 peptide


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Proteomic identification and structural basis for the interaction between sorting nexin SNX17 and PDLIM family proteins.

Healy, M.D.Sacharz, J.McNally, K.E.McConville, C.Tillu, V.A.Hall, R.J.Chilton, M.Cullen, P.J.Mobli, M.Ghai, R.Stroud, D.A.Collins, B.M.

(2022) Structure 30: 1590-1602.e6

  • DOI: https://doi.org/10.1016/j.str.2022.10.001
  • Primary Citation of Related Structures:  
    7RM8

  • PubMed Abstract: 

    The sorting nexin SNX17 controls endosomal recycling of transmembrane cargo proteins including integrins, the amyloid precursor protein, and lipoprotein receptors. This requires association with the Commander trafficking complex and depends on the C terminus of SNX17 through unknown mechanisms. Using proteomics, we find that the SNX17 C terminus is sufficient for Commander interaction and also associates with members of the PDZ and LIM domain (PDLIM) family. SNX17 contains a type III PDZ binding motif that binds specifically to the PDLIM proteins. The structure of the PDLIM7 PDZ domain bound to the SNX17 C terminus reveals an unconventional perpendicular peptide interaction mediated by electrostatic contacts and a uniquely conserved proline-containing loop sequence in the PDLIM protein family. Our results define the mechanism of SNX17-PDLIM interaction and suggest that the PDLIM proteins may play a role in regulating the activity of SNX17 in conjunction with Commander and actin-rich endosomal trafficking domains.


  • Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 4 of PDZ and LIM domain protein 7,Sorting nexin-17 fusion112Homo sapiensMutation(s): 0 
Gene Names: PDLIM7ENIGMASNX17KIAA0064
UniProt & NIH Common Fund Data Resources
Find proteins for Q15036 (Homo sapiens)
Explore Q15036 
Go to UniProtKB:  Q15036
PHAROS:  Q15036
GTEx:  ENSG00000115234 
Find proteins for Q9NR12 (Homo sapiens)
Explore Q9NR12 
Go to UniProtKB:  Q9NR12
PHAROS:  Q9NR12
GTEx:  ENSG00000196923 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9NR12Q15036
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 20 
  • Conformers Submitted: 20 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1156732
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1136021
Australian Research Council (ARC)AustraliaDP190101177
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1162597
Medical Research Council (MRC, United Kingdom)United KingdomMR/P018807/1
Wellcome TrustUnited Kingdom104568/Z/14/Z
Wellcome TrustUnited Kingdom220260/Z/20/Z
Royal SocietyUnited KingdomRSRP/R1/211004

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references