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


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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 ...

    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

    School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK. Electronic address: pete.cullen@bristol.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence 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)
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Go to UniProtKB:  Q9Y6G5
PHAROS:  Q9Y6G5
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UniProt GroupQ9Y6G5
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Entity ID: 2
MoleculeChainsSequence 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)
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Go to UniProtKB:  Q9P000
PHAROS:  Q9P000
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UniProt GroupQ9P000
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Entity ID: 3
MoleculeChainsSequence 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)
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UniProt GroupQ9GZQ3
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Entity ID: 4
MoleculeChainsSequence 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
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UniProt GroupQ86VX2
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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

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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