6XS8

Crystal structure of Chaetomium thermophilum Vps29 complexed with RaPID-derived cyclic peptide RT-D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex.

Chen, K.E.Guo, Q.Hill, T.A.Cui, Y.Kendall, A.K.Yang, Z.Hall, R.J.Healy, M.D.Sacharz, J.Norwood, S.J.Fonseka, S.Xie, B.Reid, R.C.Leneva, N.Parton, R.G.Ghai, R.Stroud, D.A.Fairlie, D.P.Suga, H.Jackson, L.P.Teasdale, R.D.Passioura, T.Collins, B.M.

(2021) Sci Adv 7: eabg4007-eabg4007

  • DOI: https://doi.org/10.1126/sciadv.abg4007
  • Primary Citation of Related Structures:  
    6XS5, 6XS7, 6XS8, 6XS9, 6XSA

  • PubMed Abstract: 

    The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and bacterial pathogens can hijack the complex during cellular infection. To modulate and probe its function, we have created a novel series of macrocyclic peptides that bind retromer with high affinity and specificity. Crystal structures show that most of the cyclic peptides bind to Vps29 via a Pro-Leu–containing sequence, structurally mimicking known interactors such as TBC1D5 and blocking their interaction with retromer in vitro and in cells. By contrast, macrocyclic peptide RT-L4 binds retromer at the Vps35-Vps26 interface and is a more effective molecular chaperone than reported small molecules, suggesting a new therapeutic avenue for targeting retromer. Last, tagged peptides can be used to probe the cellular localization of retromer and its functional interactions in cells, providing novel tools for studying retromer function.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 29203Thermochaetoides thermophilaMutation(s): 0 
UniProt
Find proteins for G0RZB5 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RZB5 
Go to UniProtKB:  G0RZB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0RZB5
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
48V-DTY-GLY-TYR-ASP-PRO-LEU-GLY-LEU-LYS-TYR-PHE-ALA13synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.52α = 90
b = 47.52β = 90
c = 170.99γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP160101743

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-12-15
    Changes: Advisory, Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description