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- PDB-7u6f: Mouse retromer (VPS26/VPS35/VPS29) heterotrimers -

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Basic information

Entry
Database: PDB / ID: 7u6f
TitleMouse retromer (VPS26/VPS35/VPS29) heterotrimers
Components(Vacuolar protein sorting-associated protein ...) x 3
KeywordsTRANSPORT PROTEIN / retromer / membrane trafficking / endosomal trafficking / membrane coat complexes / PROTEIN TRANSPORT
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / vacuolar protein processing ...WNT ligand biogenesis and trafficking / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / vacuolar protein processing / retromer, cargo-selective complex / mitochondrion to lysosome vesicle-mediated transport / Golgi to vacuole transport / protein localization to organelle / negative regulation of lysosomal protein catabolic process / positive regulation of locomotion involved in locomotory behavior / negative regulation of late endosome to lysosome transport / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / retromer complex / vesicle-mediated transport in synapse / voluntary musculoskeletal movement / mitochondrial fragmentation involved in apoptotic process / transcytosis / dopaminergic synapse / regulation of synapse maturation / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / lysosome organization / positive regulation of mitochondrial fission / regulation of postsynapse assembly / D1 dopamine receptor binding / intracellular protein transport / protein destabilization / modulation of chemical synaptic transmission / negative regulation of inflammatory response / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / protein transport / presynapse / vesicle / early endosome / lysosome / postsynapse / endosome / neuron projection / endosome membrane / postsynaptic density / negative regulation of gene expression / neuronal cell body / synapse / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / mitochondrion / metal ion binding / membrane / cytoplasm / cytosol
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: 4.9 Å
AuthorsKendall, A.K. / Chandra, M. / Jackson, L.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J Biol Chem / Year: 2022
Title: Improved mammalian retromer cryo-EM structures reveal a new assembly interface.
Authors: Amy K Kendall / Mintu Chandra / Boyang Xie / William Wan / Lauren P Jackson /
Abstract: Retromer (VPS26/VPS35/VPS29 subunits) assembles with multiple sorting nexin proteins on membranes to mediate endosomal recycling of transmembrane protein cargoes. Retromer has been implicated in ...Retromer (VPS26/VPS35/VPS29 subunits) assembles with multiple sorting nexin proteins on membranes to mediate endosomal recycling of transmembrane protein cargoes. Retromer has been implicated in other cellular processes, including mitochondrial homeostasis, nutrient sensing, autophagy, and fission events. Mechanisms for mammalian retromer assembly remain undefined, and retromer engages multiple sorting nexin proteins to sort cargoes to different destinations. Published structures demonstrate mammalian retromer forms oligomers in vitro, but several structures were poorly resolved. We report here improved retromer oligomer structures using single-particle cryo-EM by combining data collected from tilted specimens with multiple advancements in data processing, including using a 3D starting model for enhanced automated particle picking in RELION. We used a retromer mutant (3KE retromer) that breaks VPS35-mediated interfaces to determine a structure of a new assembly interface formed by the VPS26A and VPS35 N-termini. The interface reveals how an N-terminal VPS26A arrestin saddle can link retromer chains by engaging a neighboring VPS35 N- terminus, on the opposite side from the well-characterized C-VPS26/N-VPS35 interaction observed within heterotrimers. The new interaction interface exhibits substantial buried surface area (∼7000 Å) and further suggests that metazoan retromer may serve as an adaptable scaffold.
History
DepositionMar 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D1: Vacuolar protein sorting-associated protein 35
B3: Vacuolar protein sorting-associated protein 26A
B4: Vacuolar protein sorting-associated protein 29
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,53131
Polymers150,5113
Non-polymers2,02028
Water1,27971
1


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

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Components

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Vacuolar protein sorting-associated protein ... , 3 types, 3 molecules D1B3B4

#1: Protein Vacuolar protein sorting-associated protein 35 / 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 / 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 / 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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Non-polymers , 4 types, 99 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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) heterotrimer / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding 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 FIELD / Nominal defocus max: 4700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 72 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43808 / Symmetry type: POINT

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