8F2R | pdb_00008f2r

Human CCC complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8F2R

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 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.

Macromolecule Content 

  • Total Structure Weight: 206.84 kDa 
  • Atom Count: 14,504 
  • Modeled Residue Count: 1,837 
  • Deposited Residue Count: 1,837 
  • Unique protein chains: 10

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 1187Homo sapiensMutation(s): 0 
Gene Names: COMMD1C2orf5MURR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N668 (Homo sapiens)
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Go to UniProtKB:  Q8N668
PHAROS:  Q8N668
GTEx:  ENSG00000173163 
Entity Groups
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UniProt GroupQ8N668
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 2199Homo sapiensMutation(s): 0 
Gene Names: COMMD2HSPC042My004
UniProt & NIH Common Fund Data Resources
Find proteins for Q86X83 (Homo sapiens)
Explore Q86X83 
Go to UniProtKB:  Q86X83
PHAROS:  Q86X83
GTEx:  ENSG00000114744 
Entity Groups
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UniProt GroupQ86X83
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 3195Homo sapiensMutation(s): 0 
Gene Names: COMMD3BUPC10orf8
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Find proteins for Q9UBI1 (Homo sapiens)
Explore Q9UBI1 
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PHAROS:  Q9UBI1
GTEx:  ENSG00000148444 
Entity Groups
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UniProt GroupQ9UBI1
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 4199Homo sapiensMutation(s): 0 
Gene Names: COMMD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0A8 (Homo sapiens)
Explore Q9H0A8 
Go to UniProtKB:  Q9H0A8
PHAROS:  Q9H0A8
GTEx:  ENSG00000140365 
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UniProt GroupQ9H0A8
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 5205Homo sapiensMutation(s): 0 
Gene Names: COMMD5HT002
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Find proteins for Q9GZQ3 (Homo sapiens)
Explore Q9GZQ3 
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PHAROS:  Q9GZQ3
GTEx:  ENSG00000170619 
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UniProt GroupQ9GZQ3
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 677Homo sapiensMutation(s): 0 
Gene Names: COMMD6MSTP076
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Find proteins for Q7Z4G1 (Homo sapiens)
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PHAROS:  Q7Z4G1
GTEx:  ENSG00000188243 
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UniProt GroupQ7Z4G1
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 7200Homo sapiensMutation(s): 0 
Gene Names: COMMD7C20orf92
UniProt & NIH Common Fund Data Resources
Find proteins for Q86VX2 (Homo sapiens)
Explore Q86VX2 
Go to UniProtKB:  Q86VX2
PHAROS:  Q86VX2
GTEx:  ENSG00000149600 
Entity Groups
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UniProt GroupQ86VX2
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 8179Homo sapiensMutation(s): 0 
Gene Names: COMMD8MDS022
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Find proteins for Q9NX08 (Homo sapiens)
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PHAROS:  Q9NX08
GTEx:  ENSG00000169019 
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UniProt GroupQ9NX08
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 9198Homo sapiensMutation(s): 0 
Gene Names: COMMD9HSPC166
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P000 (Homo sapiens)
Explore Q9P000 
Go to UniProtKB:  Q9P000
PHAROS:  Q9P000
GTEx:  ENSG00000110442 
Entity Groups
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UniProt GroupQ9P000
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
COMM domain-containing protein 10198Homo sapiensMutation(s): 0 
Gene Names: COMMD10HSPC305PTD002
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6G5 (Homo sapiens)
Explore Q9Y6G5 
Go to UniProtKB:  Q9Y6G5
PHAROS:  Q9Y6G5
GTEx:  ENSG00000145781 
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UniProt GroupQ9Y6G5
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom104568/Z/14/Z
Wellcome TrustUnited Kingdom220260/Z/20/Z
Wellcome TrustUnited Kingdom220480/Z/20/Z
Medical Research Council (MRC, United Kingdom)United KingdomMR/L007363/1
Medical Research Council (MRC, United Kingdom)United KingdomMR/P018807/1
The Lister Institute of Preventive MedicineUnited Kingdom--
Royal SocietyUnited KingdomRSRP/R1/211004
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1136021
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1156493

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection