8P0V

Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure and interactions of the endogenous human Commander complex.

Laulumaa, S.Kumpula, E.P.Huiskonen, J.T.Varjosalo, M.

(2024) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-024-01246-1
  • Primary Citation of Related Structures:  
    8P0V, 8P0W, 8P0X

  • PubMed Abstract: 

    The Commander complex, a 16-protein assembly, plays multiple roles in cell homeostasis, cell cycle and immune response. It consists of copper-metabolism Murr1 domain proteins (COMMD1-10), coiled-coil domain-containing proteins (CCDC22 and CCDC93), DENND10 and the Retriever subcomplex (VPS26C, VPS29 and VPS35L), all expressed ubiquitously in the body and linked to various diseases. Here, we report the structure and key interactions of the endogenous human Commander complex by cryogenic-electron microscopy and mass spectrometry-based proteomics. The complex consists of a stable core of COMMD1-10 and an effector containing DENND10 and Retriever, scaffolded together by CCDC22 and CCDC93. We establish the composition of Commander and reveal major interaction interfaces. These findings clarify its roles in intracellular transport, and uncover a strong association with cilium assembly, and centrosome and centriole functions.


  • Organizational Affiliation

    Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, Helsinki, Finland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 93A [auth K]631Homo sapiensMutation(s): 0 
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Find proteins for Q567U6 (Homo sapiens)
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Go to UniProtKB:  Q567U6
PHAROS:  Q567U6
GTEx:  ENSG00000125633 
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UniProt GroupQ567U6
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 22B [auth L]627Homo sapiensMutation(s): 0 
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Find proteins for O60826 (Homo sapiens)
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Go to UniProtKB:  O60826
PHAROS:  O60826
GTEx:  ENSG00000101997 
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UniProt GroupO60826
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DENN domain-containing protein 10C [auth M]357Homo sapiensMutation(s): 0 
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Go to UniProtKB:  Q8TCE6
GTEx:  ENSG00000119979 
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UniProt GroupQ8TCE6
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 29D [auth N]182Homo sapiensMutation(s): 0 
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Find proteins for Q9UBQ0 (Homo sapiens)
Explore Q9UBQ0 
Go to UniProtKB:  Q9UBQ0
PHAROS:  Q9UBQ0
GTEx:  ENSG00000111237 
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UniProt GroupQ9UBQ0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
VPS35 endosomal protein-sorting factor-likeE [auth O]963Homo sapiensMutation(s): 0 
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Explore Q7Z3J2 
Go to UniProtKB:  Q7Z3J2
PHAROS:  Q7Z3J2
GTEx:  ENSG00000103544 
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UniProt GroupQ7Z3J2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.1.1
MODEL REFINEMENTPHENIX1.20

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland288475
Academy of FinlandFinland319303
Academy of FinlandFinland336470
Academy of FinlandFinland314669

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release