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

Michael D Healy, Kerrie E McNally*, Rebeka Butkovič, Molly Chilton, Kohji Kato, Joanna Sacharz, Calum McConville, Edmund R R Moody, Shrestha Shaw, Vicente J Planelles-Herrero, Sathish K N Yadav, Jennifer Ross, Ufuk Borucu, Catherine S Palmer, Kai-En Chen, Tristan I Croll, Ryan J Hall, Nikeisha J Caruana, Rajesh Ghai, Thi H D NguyenKate J Heesom, Shinji Saitoh, Imre Berger, Christiane Schaffitzel, Tom A Williams, David A Stroud, Emmanuel Derivery, Brett M Collins, Peter J Cullen

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

22 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)2219-2237.e29
Number of pages49
JournalCell
Volume186
Issue number10
DOIs
Publication statusPublished - 11 May 2023

Bibliographical note

Funding Information:
We thank the Wolfson Bioimaging Facility, Proteomics Facility, and GW4 Facility for Electron Cryo-Microscopy funded by the Wellcome Trust (202904/Z/16/Z and 206181/Z/17/Z) and BBSRC (BB/R000484/1) at the University of Bristol, and the Advanced Computing Research Centre. We acknowledge the Medical Research Council (MRC) - LMB Electron Microscopy Facility for EM sample preparation and data collection and thank Jake Grimmett and Toby Darling for their support. We acknowledge the Bio21 Mass Spectrometry and Proteomics Facility (MMSPF) for the provision of instrumentation and technical support. We thank Dr. Alun Jones (IMB, UQ) for assistance with mass spectrometry and the University of Queensland Remote Operation Crystallization and X-ray (UQ ROCX) Facility and Dr. Kasun Athukorala Arachchige for protein crystallization. X-ray data were collected on the MX2 microfocus beamline at the Australian Synchrotron. We thank Dr. Andrew Carter (MRC-LMB) for suggesting biGbac. P.J.C. is supported by the Wellcome Trust (104568/Z/14/Z and 220260/Z/20/Z), the MRC (MR/L007363/1 and MR/P018807/1), the Lister Institute of Preventive Medicine, and the Royal Society Noreen Murray Research Professorship (RSRP/R1/211004). B.M.C. is supported by an Investigator Grant, Senior Research Fellowship and Project Grant from the National Health and MRC (APP2016410, APP1136021 and APP1156493). D.A.S. is supported by an Investigator Fellowship and Project Grant from the National Health and MRC (APP2009732 and APP1156732). K.E.M. is supported by the Wellcome Trust through a Sir Henry Wellcome Postdoctoral Fellowship (220480/Z/20/Z). M.D.H. was supported by the AINSE PGRA, and R.B. and S. Shaw. were supported by the EndoConnect European Research Training Network (No. 953489). C.S. and I.B. are Investigators of the Wellcome Trust (210701/Z/18/Z; 106115/Z/14/Z). T.A.W. is supported by a Royal Society University Research Fellowship (URF/R/201024) and the Moore Foundation. E.D. is funded by the MRC (MC_UP_1201/13) and Human Frontier Science Program (Career Development Award CDA00034/2017). We also thank Milot Mirdita, Sergey Ovchinnikov, Martin Steinegger, and the Colab-Fold team for making their AlphaFold2 modeling pipeline publicly available. M.D.H. K.E.M. D.A.S. B.M.C. and P.J.C. designed research; M.D.H. K.-E.C. R.J.H. and R.G. performed X-ray crystallography, ITC analysis, and AlphaFold2 modeling; K.E.M. and M.C. performed insect cell purification; K.E.M. V.J.P.-H. S.K.N.Y. J.R. U.B. performed Retriever cryo-EM and data analysis; K.E.M. V.J.P-H. T.H.D.N. performed CCC complex cryo-EM and data analysis; K.E.M. R.B. K.K. S. Shaw. J.S. C.M. C.S.P. T.I.C. N.J.C. and K.J.H. performed cell-based analysis and proteomics; E.R.R.M. and T.A.W. performed evolutionary analysis; K.E.M. S. Saitoh. E.D. T.A.W. I.B. C.S. D.A.S. E.D. B.M.C. and P.J.C. acquired funding; and M.D.H. K.E.M. R.B. B.M.C. and P.J.C. wrote the paper guided by all authors. The authors declare that they have no conflicts of interest. We support inclusive, diverse, and equitable conduct of research.

Funding Information:
We thank the Wolfson Bioimaging Facility, Proteomics Facility, and GW4 Facility for Electron Cryo-Microscopy funded by the Wellcome Trust ( 202904/Z/16/Z and 206181/Z/17/Z ) and BBSRC ( BB/R000484/1 ) at the University of Bristol , and the Advanced Computing Research Centre . We acknowledge the Medical Research Council (MRC) - LMB Electron Microscopy Facility for EM sample preparation and data collection and thank Jake Grimmett and Toby Darling for their support. We acknowledge the Bio21 Mass Spectrometry and Proteomics Facility (MMSPF) for the provision of instrumentation and technical support. We thank Dr. Alun Jones (IMB, UQ) for assistance with mass spectrometry and the University of Queensland Remote Operation Crystallization and X-ray (UQ ROCX) Facility and Dr. Kasun Athukorala Arachchige for protein crystallization. X-ray data were collected on the MX2 microfocus beamline at the Australian Synchrotron. We thank Dr. Andrew Carter (MRC-LMB) for suggesting biGbac. P.J.C. is supported by the Wellcome Trust ( 104568/Z/14/Z and 220260/Z/20/Z ), the MRC ( MR/L007363/1 and MR/P018807/1 ), the Lister Institute of Preventive Medicine , and the Royal Society Noreen Murray Research Professorship ( RSRP/R1/211004 ). B.M.C. is supported by an Investigator Grant , Senior Research Fellowship and Project Grant from the National Health and MRC ( APP2016410 , APP1136021 and APP1156493 ). D.A.S. is supported by an Investigator Fellowship and Project Grant from the National Health and MRC ( APP2009732 and APP1156732 ). K.E.M. is supported by the Wellcome Trust through a Sir Henry Wellcome Postdoctoral Fellowship ( 220480/Z/20/Z ). M.D.H. was supported by the AINSE PGRA, and R.B. and S. Shaw. were supported by the EndoConnect European Research Training Network (No. 953489 ). C.S. and I.B. are Investigators of the Wellcome Trust ( 210701/Z/18/Z ; 106115/Z/14/Z ). T.A.W. is supported by a Royal Society University Research Fellowship ( URF/R/201024 ) and the Moore Foundation . E.D. is funded by the MRC ( MC_UP_1201/13 ) and Human Frontier Science Program (Career Development Award CDA00034/2017 ). We also thank Milot Mirdita, Sergey Ovchinnikov, Martin Steinegger, and the Colab-Fold team for making their AlphaFold2 modeling pipeline publicly available.

Publisher Copyright:
© 2023 The Author(s)

Keywords

  • Humans
  • Abnormalities, Multiple
  • Craniofacial Abnormalities
  • Endosomes/metabolism
  • Protein Transport
  • Proteins/metabolism
  • Multiprotein Complexes/metabolism

Fingerprint

Dive into the research topics of 'Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome'. Together they form a unique fingerprint.

Cite this