8SYO

Human Retriever VPS35L/VPS29/VPS26C Complex (Composite Map)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural organization of the retriever-CCC endosomal recycling complex.

Boesch, D.J.Singla, A.Han, Y.Kramer, D.A.Liu, Q.Suzuki, K.Juneja, P.Zhao, X.Long, X.Medlyn, M.J.Billadeau, D.D.Chen, Z.Chen, B.Burstein, E.

(2023) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-023-01184-4
  • Primary Citation of Related Structures:  
    8SYM, 8SYN, 8SYO

  • PubMed Abstract: 

    The recycling of membrane proteins from endosomes to the cell surface is vital for cell signaling and survival. Retriever, a trimeric complex of vacuolar protein-sorting-associated protein (VPS)35L, VPS26C and VPS29, together with the CCC complex comprising coiled-coil domain-containing (CCDC)22, CCDC93 and copper metabolism domain-containing (COMMD) proteins, plays a crucial role in this process. The precise mechanisms underlying retriever assembly and its interaction with CCC have remained elusive. Here, we present a high-resolution structure of retriever in humans determined using cryogenic electron microscopy. The structure reveals a unique assembly mechanism, distinguishing it from its remotely related paralog retromer. By combining AlphaFold predictions and biochemical, cellular and proteomic analyses, we further elucidate the structural organization of the entire retriever-CCC complex across evolution and uncover how cancer-associated mutations in humans disrupt complex formation and impair membrane protein homeostasis. These findings provide a fundamental framework for understanding the biological and pathological implications associated with retriever-CCC-mediated endosomal recycling.


  • Organizational Affiliation

    Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VPS35 endosomal protein-sorting factor-like963Homo sapiensMutation(s): 0 
Gene Names: VPS35LC16orf62101F10.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3J2 (Homo sapiens)
Explore Q7Z3J2 
Go to UniProtKB:  Q7Z3J2
PHAROS:  Q7Z3J2
GTEx:  ENSG00000103544 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z3J2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 29205Homo sapiensMutation(s): 0 
Gene Names: VPS29DC15DC7MDS007
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBQ0 (Homo sapiens)
Explore Q9UBQ0 
Go to UniProtKB:  Q9UBQ0
PHAROS:  Q9UBQ0
GTEx:  ENSG00000111237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBQ0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 26C297Homo sapiensMutation(s): 0 
Gene Names: VPS26CDCRADSCR3DSCRA
UniProt & NIH Common Fund Data Resources
Find proteins for O14972 (Homo sapiens)
Explore O14972 
Go to UniProtKB:  O14972
PHAROS:  O14972
GTEx:  ENSG00000157538 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14972
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM128786
National Science Foundation (NSF, United States)United StatesCAREER 2047640

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-12-13
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Database references