8ESE | pdb_00008ese

Crystal structure of human Vps29 bound to a peptide from Vps35L

• PDB DOI: https://doi.org/10.2210/pdb8ESE/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-13 Released: 2023-05-24 
• Deposition Author(s): Healy, M.D., Collins, B.M.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

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

• PubMed: 37172566 
• 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.
School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK; MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK. Electronic address: [e-mail].
School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK.
Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
School of Biological Sciences, University of Bristol, BS8 1TD Bristol, UK.
MRC Laboratory of Molecular Biology, CB2 0QH Cambridge, UK.
Cambridge Institute for Medical Research, University of Cambridge, CB2 0XY Cambridge, UK.
Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; Institute of Health and Sport (iHeS), Victoria University, Melbourne, VIC Australia.
Proteomics Facility, School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK.
Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences and Medical School, Nagoya, Japan.
School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK; Max Planck Bristol Centre for Minimal Biology, Department of Chemistry, University of Bristol, BS8 1TS Bristol, UK.
Department of Biochemistry and Pharmacology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC Australia.
Centre for Cell Biology of Chronic Disease, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia. Electronic address: [e-mail].
School of Biochemistry, Biomedical Sciences Building, University of Bristol, BS8 1TD Bristol, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 23.36 kDa 
• Atom Count: 1,767 
• Modeled Residue Count: 198 
• Deposited Residue Count: 207 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VPS35 endosomal protein-sorting factor-like	A [auth X]	23	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3J2 (Homo sapiens) Explore Q7Z3J2  Go to UniProtKB:  Q7Z3J2
PHAROS:  Q7Z3J2 GTEx:  ENSG00000103544

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 29	B [auth Z]	184	Homo sapiens	Mutation(s): 0  Gene Names: VPS29, DC15, DC7, MDS007
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBQ0 (Homo sapiens) Explore Q9UBQ0  Go to UniProtKB:  Q9UBQ0
PHAROS:  Q9UBQ0 GTEx:  ENSG00000111237

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.719	α = 90
b = 55.285	β = 90
c = 82.644	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-05-24 
Deposition Author(s): Healy, M.D., Collins, B.M.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

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