8ESD

Crystal structure of COMMD7-COMMD9-COMMD5-COMMD10 tetramer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome.

Healy, M.D.McNally, K.E.Butkovic, R.Chilton, M.Kato, K.Sacharz, J.McConville, C.Moody, E.R.R.Shaw, S.Planelles-Herrero, V.J.Yadav, S.K.N.Ross, J.Borucu, U.Palmer, C.S.Chen, K.E.Croll, T.I.Hall, R.J.Caruana, N.J.Ghai, R.Nguyen, T.H.D.Heesom, K.J.Saitoh, S.Berger, I.Schaffitzel, C.Williams, T.A.Stroud, D.A.Derivery, E.Collins, B.M.Cullen, P.J.

(2023) Cell 186: 2219-2237.e29

  • DOI: https://doi.org/10.1016/j.cell.2023.04.003
  • Primary Citation of Related Structures:  
    8ESD, 8ESE, 8F2R, 8F2U

  • PubMed Abstract: 

    The Commander complex is required for endosomal recycling of diverse transmembrane cargos and is mutated in Ritscher-Schinzel syndrome. It comprises two sub-assemblies: Retriever composed of VPS35L, VPS26C, and VPS29; and the CCC complex which contains twelve subunits: COMMD1-COMMD10 and the coiled-coil domain-containing (CCDC) proteins CCDC22 and CCDC93. Combining X-ray crystallography, electron cryomicroscopy, and in silico predictions, we have assembled a complete structural model of Commander. Retriever is distantly related to the endosomal Retromer complex but has unique features preventing the shared VPS29 subunit from interacting with Retromer-associated factors. The COMMD proteins form a distinctive hetero-decameric ring stabilized by extensive interactions with CCDC22 and CCDC93. These adopt a coiled-coil structure that connects the CCC and Retriever assemblies and recruits a 16th subunit, DENND10, to form the complete Commander complex. The structure allows mapping of disease-causing mutations and reveals the molecular features required for the function of this evolutionarily conserved trafficking machinery.


  • Organizational Affiliation

    Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 10A [auth T]191Homo sapiensMutation(s): 0 
Gene Names: COMMD10HSPC305PTD002
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Find proteins for Q9Y6G5 (Homo sapiens)
Explore Q9Y6G5 
Go to UniProtKB:  Q9Y6G5
PHAROS:  Q9Y6G5
GTEx:  ENSG00000145781 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6G5
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 9B [auth N]194Homo sapiensMutation(s): 0 
Gene Names: COMMD9HSPC166
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Find proteins for Q9P000 (Homo sapiens)
Explore Q9P000 
Go to UniProtKB:  Q9P000
PHAROS:  Q9P000
GTEx:  ENSG00000110442 
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UniProt GroupQ9P000
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 5C [auth F]75Homo sapiensMutation(s): 0 
Gene Names: COMMD5HT002
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Find proteins for Q9GZQ3 (Homo sapiens)
Explore Q9GZQ3 
Go to UniProtKB:  Q9GZQ3
PHAROS:  Q9GZQ3
GTEx:  ENSG00000170619 
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UniProt GroupQ9GZQ3
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COMM domain-containing protein 7D [auth S]70Homo sapiensMutation(s): 0 
Gene Names: COMMD7C20orf92
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Find proteins for Q86VX2 (Homo sapiens)
Explore Q86VX2 
Go to UniProtKB:  Q86VX2
PHAROS:  Q86VX2
GTEx:  ENSG00000149600 
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UniProt GroupQ86VX2
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.33 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 215.191α = 90
b = 74.895β = 96.397
c = 63.632γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description