9O9I | pdb_00009o9i

Crystal structure of mouse Vps29 bound to DENND4C peptide (re-refinement)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.253 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 8VOD


Literature

Mapping of endosomal proximity proteomes reveals Retromer as a hub for RAB GTPase regulation.

Anton-Plagaro, C.Chen, K.E.Guo, Q.Liu, M.Evans, A.J.Lewis, P.A.Heesom, K.J.Wilkinson, K.A.Collins, B.M.Cullen, P.J.

(2025) Nat Commun 16: 6990-6990

  • DOI: https://doi.org/10.1038/s41467-025-61802-1
  • Primary Citation of Related Structures:  
    9O9I

  • PubMed Abstract: 

    Endosomal retrieval and recycling of integral cargo proteins is essential for cell and organism development and homeostasis and is orchestrated through a specialised endosomal nanodomain, the retrieval sub-domain. Sub-domain dysfunction is associated with human disease, but our mechanistic understanding of its function remains poorly described. Here, using proximity proteomics of retrieval sub-domain components Retromer and Retriever we identify mechanistic details of retrieval sub-domain composition and organization, including an unrecognised complexity in the interface with RAB GTPase switching. Combining X-ray crystallography and in silico predictions with biochemical and cellular analysis, we reveal that Retromer directly associates and recruits the RAB10 regulators DENND4A, DENND4C, TBC1D1, and TBC1D4, and the RAB35 regulator TBC1D13 to regulate retrieval sub-domain function. The retrieval sub-domain therefore constitutes a hub for integrating cargo recycling with the regulated switching of selected RAB GTPases. We propose this constitutes a major component of the neuroprotective role of the retrieval sub-domain.


  • Organizational Affiliation
    • School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol, UK. carlos.antonplagaro@bristol.ac.uk.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Vacuolar protein sorting-associated protein 29188Mus musculusMutation(s): 0 
Gene Names: Vps29
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QZ88 (Mus musculus)
Explore Q9QZ88 
Go to UniProtKB:  Q9QZ88
IMPC:  MGI:1928344
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QZ88
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-LYS-VAL-VAL-GLN-ARG-GLU-ASP-VAL-GLU-THR-GLY-LEU-ASP-PRO-LEU-SER-LEU18Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VZ89 (Homo sapiens)
Explore Q5VZ89 
Go to UniProtKB:  Q5VZ89
PHAROS:  Q5VZ89
GTEx:  ENSG00000137145 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5VZ89
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download Ideal Coordinates CCD File 
C [auth A]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.253 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.899α = 90
b = 42.899β = 90
c = 172.743γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP2016410
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release