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- PDB-6vac: Mouse retromer (VPS26/VPS35/VPS29) heterotrimer -

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Basic information

Entry
Database: PDB / ID: 6vac
TitleMouse retromer (VPS26/VPS35/VPS29) heterotrimer
Components
  • Vacuolar protein sorting-associated protein 26AVacuole
  • Vacuolar protein sorting-associated protein 29Vacuole
  • Vacuolar protein sorting-associated protein 35Vacuole
KeywordsPROTEIN TRANSPORT / retromer / membrane trafficking / endosomal trafficking / membrane coat complexes
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / regulation of dendritic spine maintenance / tubular endosome / mitochondrion to lysosome vesicle-mediated transport ...WNT ligand biogenesis and trafficking / positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / regulation of dendritic spine maintenance / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / vacuolar protein processing / positive regulation of Wnt protein secretion / regulation of terminal button organization / retromer, cargo-selective complex / vesicle-mediated transport in synapse / protein localization to organelle / negative regulation of late endosome to lysosome transport / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / Golgi to vacuole transport / dopaminergic synapse / mitochondrial fragmentation involved in apoptotic process / regulation of protein metabolic process / retromer complex / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / regulation of synapse maturation / voluntary musculoskeletal movement / transcytosis / endocytic recycling / positive regulation of protein localization to cell periphery / retrograde transport, endosome to Golgi / regulation of mitochondrion organization / positive regulation of mitochondrial fission / lysosome organization / D1 dopamine receptor binding / intracellular protein transport / modulation of chemical synaptic transmission / protein destabilization / regulation of protein stability / negative regulation of inflammatory response / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / late endosome / presynapse / postsynapse / vesicle / postsynaptic density / lysosome / early endosome / endosome membrane / endosome / neuron projection / negative regulation of gene expression / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / synapse / positive regulation of gene expression / perinuclear region of cytoplasm / mitochondrion / membrane / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Arrestin-like, C-terminal ...Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Arrestin-like, C-terminal / Metallo-dependent phosphatase-like / Armadillo-type fold
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 26A / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsKendall, A.K. / Jackson, L.P.
Funding support1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: Structure / Year: 2020
Title: Mammalian Retromer Is an Adaptable Scaffold for Cargo Sorting from Endosomes.
Authors: Amy K Kendall / Boyang Xie / Peng Xu / Jue Wang / Rodger Burcham / Meredith N Frazier / Elad Binshtein / Hui Wei / Todd R Graham / Terunaga Nakagawa / Lauren P Jackson /
Abstract: Metazoan retromer (VPS26/VPS35/VPS29) associates with sorting nexins on endosomal tubules to sort proteins to the trans-Golgi network or plasma membrane. Mechanisms of metazoan retromer assembly ...Metazoan retromer (VPS26/VPS35/VPS29) associates with sorting nexins on endosomal tubules to sort proteins to the trans-Golgi network or plasma membrane. Mechanisms of metazoan retromer assembly remain undefined. We combine single-particle cryoelectron microscopy with biophysical methods to uncover multiple oligomer structures. 2D class averages reveal mammalian heterotrimers; dimers of trimers; tetramers of trimers; and flat chains. These species are further supported by biophysical solution studies. We provide reconstructions of all species, including key sub-structures (∼5 Å resolution). Local resolution variation suggests that heterotrimers and dimers adopt multiple conformations. Our structures identify a flexible, highly conserved electrostatic dimeric interface formed by VPS35 subunits. We generate structure-based mutants to disrupt this interface in vitro. Equivalent mutations in yeast demonstrate a mild cargo-sorting defect. Our data suggest the metazoan retromer is an adaptable and plastic scaffold that accommodates interactions with different sorting nexins to sort multiple cargoes from endosomes their final destinations.
History
DepositionDec 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 35
B: Vacuolar protein sorting-associated protein 26A
C: Vacuolar protein sorting-associated protein 29


Theoretical massNumber of molelcules
Total (without water)150,5113
Polymers150,5113
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Vacuolar protein sorting-associated protein 35 / Vacuole / Maternal-embryonic 3 / Vesicle protein sorting 35


Mass: 91821.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps35, Mem3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EQH3
#2: Protein Vacuolar protein sorting-associated protein 26A / Vacuole / H58 protein / H beta 58 / Vesicle protein sorting 26A / mVPS26


Mass: 38167.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps26a, Vps26 / Production host: Escherichia coli (E. coli) / References: UniProt: P40336
#3: Protein Vacuolar protein sorting-associated protein 29 / Vacuole / Vesicle protein sorting 29


Mass: 20521.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QZ88

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.2
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 71 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26369 / Symmetry type: POINT

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