8P0W

Structure of the human Commander complex COMMD ring


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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
COMM domain-containing protein 1190Homo sapiensMutation(s): 0 
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PHAROS:  Q8N668
GTEx:  ENSG00000173163 
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UniProt GroupQ8N668
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 2199Homo sapiensMutation(s): 0 
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PHAROS:  Q86X83
GTEx:  ENSG00000114744 
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UniProt GroupQ86X83
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 3195Homo sapiensMutation(s): 0 
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PHAROS:  Q9UBI1
GTEx:  ENSG00000148444 
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UniProt GroupQ9UBI1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 4199Homo sapiensMutation(s): 0 
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PHAROS:  Q9H0A8
GTEx:  ENSG00000140365 
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UniProt GroupQ9H0A8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 5224Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000170619 
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UniProt GroupQ9GZQ3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 685Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188243 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 7200Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000149600 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 8183Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000169019 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 9198Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110442 
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UniProt GroupQ9P000
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 10202Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145781 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 93631Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000125633 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Coiled-coil domain-containing protein 22627Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101997 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.1.1
MODEL REFINEMENTPHENIX1.20

Structure Validation

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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