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- PDB-8esd: Crystal structure of COMMD7-COMMD9-COMMD5-COMMD10 tetramer -

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Basic information

Entry
Database: PDB / ID: 8esd
TitleCrystal structure of COMMD7-COMMD9-COMMD5-COMMD10 tetramer
Components
  • COMM domain-containing protein 10
  • COMM domain-containing protein 5
  • COMM domain-containing protein 7
  • COMM domain-containing protein 9
KeywordsENDOCYTOSIS / Complex / Commander / Retriever / Commd5 / Commd7 / Commd9 / Commd10 / Commd
Function / homology
Function and homology information


negative regulation of NF-kappaB transcription factor activity / sodium ion transport / NF-kappaB binding / cholesterol homeostasis / tumor necrosis factor-mediated signaling pathway / Neddylation / cytoplasmic vesicle / secretory granule lumen / ficolin-1-rich granule lumen / negative regulation of DNA-templated transcription ...negative regulation of NF-kappaB transcription factor activity / sodium ion transport / NF-kappaB binding / cholesterol homeostasis / tumor necrosis factor-mediated signaling pathway / 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
COMM domain-containing protein 5 / COMM domain-containing protein 7 / COMM domain-containing protein 10 / : / COMMD2-7/10, HN domain / COMM domain-containing protein 9 / : / COMMD9, helical N-terminal domain / COMM domain / COMM domain / COMM domain profile.
Similarity search - Domain/homology
COMM domain-containing protein 7 / COMM domain-containing protein 5 / COMM domain-containing protein 9 / COMM domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.33 Å
AuthorsHealy, M.D. / Collins, B.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2023
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.
History
DepositionOct 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: COMM domain-containing protein 10
N: COMM domain-containing protein 9
F: COMM domain-containing protein 5
S: COMM domain-containing protein 7


Theoretical massNumber of molelcules
Total (without water)60,0954
Polymers60,0954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12100 Å2
ΔGint-90 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)215.191, 74.895, 63.632
Angle α, β, γ (deg.)90.000, 96.397, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein COMM domain-containing protein 10


Mass: 21828.939 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD10, HSPC305, PTD002 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6G5
#2: Protein COMM domain-containing protein 9


Mass: 21457.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD9, HSPC166 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P000
#3: Protein COMM domain-containing protein 5 / Hypertension-related calcium-regulated gene protein / HCaRG


Mass: 8636.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD5, HT002 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ3
#4: Protein COMM domain-containing protein 7


Mass: 8172.452 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: COMMD7, C20orf92 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86VX2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.82 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BP6

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
RfactorNum. reflection% reflection
Rfree0.2783 1349 9.9 %
Rwork0.2378 12284 -
obs0.242 13633 91.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 127.07 Å2
Refinement stepCycle: LAST / Resolution: 3.33→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 0 0 0 4089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314174
X-RAY DIFFRACTIONf_angle_d0.92225640
X-RAY DIFFRACTIONf_chiral_restr0.0413668
X-RAY DIFFRACTIONf_plane_restr0.0109716
X-RAY DIFFRACTIONf_dihedral_angle_d15.1631584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.33-3.450.42281090.3198997X-RAY DIFFRACTION74.53
3.45-3.590.36381160.2791098X-RAY DIFFRACTION81.31
3.59-3.750.3341130.27361143X-RAY DIFFRACTION85.04
3.75-3.950.34771330.2551177X-RAY DIFFRACTION88.51
3.95-4.190.27041420.22891238X-RAY DIFFRACTION93.18
4.19-4.520.27351400.21131289X-RAY DIFFRACTION96.1
4.52-4.970.23811490.1941325X-RAY DIFFRACTION98.4
4.97-5.690.30071480.23041323X-RAY DIFFRACTION98.2
5.69-7.160.30351480.29541324X-RAY DIFFRACTION98.26
7.16-38.50.23511510.22461370X-RAY DIFFRACTION98.32

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