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- PDB-8ese: Crystal structure of human Vps29 bound to a peptide from Vps35L -

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Basic information

Entry
Database: PDB / ID: 8ese
TitleCrystal structure of human Vps29 bound to a peptide from Vps35L
Components
  • VPS35 endosomal protein-sorting factor-like
  • Vacuolar protein sorting-associated protein 29Vacuole
KeywordsENDOCYTOSIS / Commander / Retriever / Vps29 / Vps35L
Function / homology
Function and homology information


retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / protein transport / early endosome / endosome membrane ...retromer, cargo-selective complex / WNT ligand biogenesis and trafficking / retromer complex / endocytic recycling / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / protein transport / early endosome / endosome membrane / endosome / intracellular membrane-bounded organelle / metal ion binding / cytosol
Similarity search - Function
VPS35 endosomal protein sorting factor-like / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
VPS35 endosomal protein-sorting factor-like / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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
X: VPS35 endosomal protein-sorting factor-like
Z: Vacuolar protein sorting-associated protein 29


Theoretical massNumber of molelcules
Total (without water)23,3622
Polymers23,3622
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-9 kcal/mol
Surface area9390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.719, 55.285, 82.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein/peptide VPS35 endosomal protein-sorting factor-like


Mass: 2635.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: B3KT69
#2: Protein Vacuolar protein sorting-associated protein 29 / Vacuole / hVPS29 / PEP11 homolog / Vesicle protein sorting 29


Mass: 20726.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS29, DC15, DC7, MDS007 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBQ0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M Bis-tris pH 5.5 and 25% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 1.35→45.95 Å / Num. obs: 44459 / % possible obs: 99.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 18.43 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.031 / Net I/σ(I): 11.3
Reflection shellResolution: 1.35→1.37 Å / Num. unique obs: 1992 / CC1/2: 0.481 / Rpim(I) all: 0.643

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XSA

6xsa


Resolution: 1.35→45.95 Å / SU ML: 0.2316 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 1999 4.57 %
Rwork0.2153 41785 -
obs0.2165 43784 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.67 Å2
Refinement stepCycle: LAST / Resolution: 1.35→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 0 191 1767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02311616
X-RAY DIFFRACTIONf_angle_d1.94452194
X-RAY DIFFRACTIONf_chiral_restr0.1373248
X-RAY DIFFRACTIONf_plane_restr0.0141279
X-RAY DIFFRACTIONf_dihedral_angle_d7.0058209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.38591310.40832750X-RAY DIFFRACTION90.77
1.38-1.420.40111430.35642998X-RAY DIFFRACTION100
1.42-1.460.3461440.36273007X-RAY DIFFRACTION99.84
1.46-1.510.35951410.36272958X-RAY DIFFRACTION98.23
1.51-1.560.27031450.25823017X-RAY DIFFRACTION99.91
1.56-1.630.25071440.23883027X-RAY DIFFRACTION100
1.63-1.70.27051440.2363011X-RAY DIFFRACTION100
1.7-1.790.28991450.2343029X-RAY DIFFRACTION99.97
1.79-1.90.28081400.23012945X-RAY DIFFRACTION96.62
1.9-2.050.2931320.25872713X-RAY DIFFRACTION89.49
2.05-2.260.28681410.2322922X-RAY DIFFRACTION95.57
2.26-2.580.20161470.19143066X-RAY DIFFRACTION98.83
2.58-3.250.1911480.18983107X-RAY DIFFRACTION99.91
3.25-45.950.20811540.1773235X-RAY DIFFRACTION99.01

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