Uhlen, M. et al. Proteomics. Tissue-based map of the human proteome. Science 347, 1260419 (2015).

Article  PubMed  Google Scholar 

Uhlen, M. et al. Towards a knowledge-based human protein atlas. Nat. Biotechnol. 28, 1248–1250 (2010).

Article  CAS  PubMed  Google Scholar 

Seaman, M. N., McCaffery, J. M. & Emr, S. D. A membrane coat complex essential for endosome-to-Golgi retrograde transport in yeast. J. Cell Biol. 142, 665–681 (1998).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Haft, C. R. et al. Human orthologs of yeast vacuolar protein sorting proteins Vps26, 29, and 35: assembly into multimeric complexes. Mol. Biol. Cell 11, 4105–4116 (2000).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Edgar, A. J. & Polak, J. M. Human homologues of yeast vacuolar protein sorting 29 and 35. Biochem. Biophys. Res. Commun. 277, 622–630 (2000).

Article  CAS  PubMed  Google Scholar 

Lucas, M. et al. Structural mechanism for cargo recognition by the retromer complex. Cell 167, 1623–1635 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Steinberg, F. et al. A global analysis of SNX27–retromer assembly and cargo specificity reveals a function in glucose and metal ion transport. Nat. Cell Biol. 15, 461–471 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Harrison, M. S. et al. A mechanism for retromer endosomal coat complex assembly with cargo. Proc. Natl Acad. Sci. USA 111, 267–272 (2014).

Article  CAS  PubMed  Google Scholar 

Yong, X. et al. SNX27–FERM–SNX1 complex structure rationalizes divergent trafficking pathways by SNX17 and SNX27. Proc. Natl Acad. Sci. USA 118, e2105510118 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Simonetti, B. et al. SNX27–retromer directly binds ESCPE-1 to transfer cargo proteins during endosomal recycling. PLoS Biol. 20, e3001601 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fjorback, A. W. et al. Retromer binds the FANSHY sorting motif in SorLA to regulate amyloid precursor protein sorting and processing. J. Neurosci. 32, 1467–1480 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gomez, T. S. & Billadeau, D. D. A FAM21-containing WASH complex regulates retromer-dependent sorting. Dev. Cell 17, 699–711 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gomez, T. S., Gorman, J. A., de Narvajas, A. A., Koenig, A. O. & Billadeau, D. D. Trafficking defects in WASH-knockout fibroblasts originate from collapsed endosomal and lysosomal networks. Mol. Biol. Cell 23, 3215–3228 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jia, D., Gomez, T. S., Billadeau, D. D. & Rosen, M. K. Multiple repeat elements within the FAM21 tail link the WASH actin regulatory complex to the retromer. Mol. Biol. Cell 23, 2352–2361 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Derivery, E. et al. The Arp2/3 activator WASH controls the fission of endosomes through a large multiprotein complex. Dev. Cell 17, 712–723 (2009).

Article  CAS  PubMed  Google Scholar 

Phillips-Krawczak, C. A. et al. COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A. Mol. Biol. Cell 26, 91–103 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Burstein, E. et al. COMMD proteins: a novel family of structural and functional homologs of MURR1. J. Biol. Chem. 280, 22222–22232 (2005).

Article  CAS  PubMed  Google Scholar 

Schou, K. B., Andersen, J. S. & Pedersen, L. B. A divergent calponin homology (NN-CH) domain defines a novel family: implications for evolution of ciliary IFT complex B proteins. Bioinformatics 30, 899–902 (2014).

Singla, A. et al. Endosomal PI3P regulation by the COMMD/CCDC22/CCDC93 (CCC) complex controls membrane protein recycling. Nat. Commun. 10, 4271 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Singla, A. et al. Regulation of murine copper homeostasis by members of the COMMD protein family. Dis. Model. Mech. 14, dmm045963 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

McNally, K. E. et al. Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling. Nat. Cell Biol. 19, 1214–1225 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bartuzi, P. et al. CCC- and WASH-mediated endosomal sorting of LDLR is required for normal clearance of circulating LDL. Nat. Commun. 7, 10961 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, H. et al. Endosomal sorting of Notch receptors through COMMD9 dependent pathways modulates Notch signaling. J. Cell Biol. 211, 605–617 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang, J. et al. DENN domain-containing protein FAM45A regulates the homeostasis of late/multivesicular endosomes. Biochim. Biophys. Acta Mol. Cell Res. 1866, 916–929 (2019).

Article  CAS  PubMed  Google Scholar 

Borchers, A. C., Langemeyer, L. & Ungermann, C. Who’s in control? Principles of Rab GTPase activation in endolysosomal membrane trafficking and beyond. J. Cell Biol. 220, e202105120 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wan, C. et al. Panorama of ancient metazoan macromolecular complexes. Nature 525, 339–344 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mallam, A. L. & Marcotte, E. M. Systems-wide studies uncover commander, a multiprotein complex essential to human development. Cell Syst. 4, 483–494 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Healy, M. D. et al. Structure of the endosomal commander complex linked to Ritscher–Schinzel syndrome. Cell 186, 2219–2237 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sanchez-Garcia, R. et al. DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Commun. Biol. 4, 874 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Collins, B. M., Skinner, C. F., Watson, P. J., Seaman, M. N. & Owen, D. J. Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer assembly. Nat. Struct. Mol. Biol. 12, 594–602 (2005).

Article  CAS  PubMed  Google Scholar 

Cleary, S. P. et al. Identification of driver genes in hepatocellular carcinoma by exome sequencing. Hepatology 58, 1693–1702 (2013).

Article  CAS  PubMed  Google Scholar 

Hecht, M., Bromberg, Y. & Rost, B. Better prediction of functional effects for sequence variants. BMC Genomics 16, S1 (2015).

Google Scholar 

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Evans, R. et al. Protein complex prediction with AlphaFold-Multimer. Preprint at bioRxiv https://doi.org/10.1101/2021.10.04.463034 (2022).

Wu, X. et al. Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate. Proc. Natl Acad. Sci. USA 108, 18672–18677 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Healy, M. D. et al. Structural insights into the architecture and membrane interactions of the conserved COMMD proteins. eLife 7, e35898 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Voineagu, I. et al. CCDC22: a novel candidate gene for syndromic X-linked intellectual disability. Mol. Psychiatry 17, 4–7 (2012).

Article  CAS  PubMed  Google Scholar 

Kolanczyk, M. et al. Missense variant in CCDC22 causes X-linked recessive intellectual disability with features of Ritscher–Schinzel/3C syndrome. Eur. J. Hum. Genet. 23, 633–638 (2014).

Kato, K. et al. Biallelic VPS35L pathogenic variants cause 3C/Ritscher–Schinzel-like syndrome through dysfunction of retriever complex. J. Med. Genet. 57, 245–253 (2020).