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Open data
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Basic information
Entry | Database: PDB / ID: 8esd | ||||||
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Title | Crystal structure of COMMD7-COMMD9-COMMD5-COMMD10 tetramer | ||||||
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![]() | ENDOCYTOSIS / Complex / Commander / Retriever / Commd5 / Commd7 / Commd9 / Commd10 / Commd | ||||||
Function / homology | ![]() sodium ion transport / negative regulation of NF-kappaB transcription factor activity / NF-kappaB binding / tumor necrosis factor-mediated signaling pathway / cholesterol homeostasis / Neddylation / cytoplasmic vesicle / secretory granule lumen / ficolin-1-rich granule lumen / negative regulation of DNA-templated transcription ...sodium ion transport / negative regulation of NF-kappaB transcription factor activity / NF-kappaB binding / tumor necrosis factor-mediated signaling pathway / cholesterol homeostasis / Neddylation / cytoplasmic vesicle / secretory granule lumen / ficolin-1-rich granule lumen / negative regulation of DNA-templated transcription / Neutrophil degranulation / Golgi apparatus / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Healy, M.D. / Collins, B.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure of the endosomal Commander complex linked to Ritscher-Schinzel syndrome. Authors: 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 / ...Authors: 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 Nguyen / Kate J Heesom / Shinji Saitoh / Imre Berger / Christiane Schaffitzel / Tom A Williams / David A Stroud / Emmanuel Derivery / Brett M Collins / Peter J Cullen / ![]() ![]() ![]() 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, ...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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.5 KB | Display | ![]() |
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PDB format | ![]() | 89.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.3 KB | Display | ![]() |
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Full document | ![]() | 456.3 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eseC ![]() 8f2rC ![]() 8f2uC ![]() 6bp6S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 21828.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 21457.607 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 8636.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 8172.452 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.37 Å3/Da / Density % sol: 71.82 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 2 uM crown ether and 10% glycerol and grown in 22% ethanol and 5 mM EDTA |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 3.13→48.52 Å / Num. obs: 16930 / % possible obs: 96.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 103.34 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.08 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 3.13→3.35 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2673 / CC1/2: 0.56 / Rpim(I) all: 0.908 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BP6 Resolution: 3.33→38.5 Å / SU ML: 0.4188 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.9287 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 127.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.33→38.5 Å
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Refine LS restraints |
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LS refinement shell |
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