+Open data
-Basic information
Entry | Database: PDB / ID: 7u6f | ||||||
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Title | Mouse retromer (VPS26/VPS35/VPS29) heterotrimers | ||||||
Components | (Vacuolar protein sorting-associated protein ...) x 3 | ||||||
Keywords | TRANSPORT PROTEIN / retromer / membrane trafficking / endosomal trafficking / membrane coat complexes / PROTEIN TRANSPORT | ||||||
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 / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / 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 / regulation of postsynapse assembly / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion / regulation of terminal button organization / retromer, cargo-selective complex / vacuolar protein processing / 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 / retromer complex / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / dopaminergic synapse / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of synapse maturation / voluntary musculoskeletal movement / transcytosis / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / positive regulation of mitochondrial fission / lysosome organization / 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 / presynapse / postsynapse / vesicle / postsynaptic density / lysosome / early endosome / endosome membrane / endosome / neuron projection / negative regulation of gene expression / neuronal cell body / glutamatergic synapse / synapse / positive regulation of gene expression / perinuclear region of cytoplasm / mitochondrion / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||
Authors | Kendall, A.K. / Chandra, M. / Jackson, L.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u6f.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u6f.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7u6f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u6f_validation.pdf.gz | 924.6 KB | Display | wwPDB validaton report |
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Full document | 7u6f_full_validation.pdf.gz | 966.7 KB | Display | |
Data in XML | 7u6f_validation.xml.gz | 43.7 KB | Display | |
Data in CIF | 7u6f_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/7u6f ftp://data.pdbj.org/pub/pdb/validation_reports/u6/7u6f | HTTPS FTP |
-Related structure data
Related structure data | M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Vacuolar protein sorting-associated protein ... , 3 types, 3 molecules D1B3B4
#1: Protein | 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 | ||
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#2: Protein | 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 | | 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 |
-Non-polymers , 4 types, 99 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mouse retromer (VPS26/VPS35/VPS29) heterotrimer / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4700 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 72 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43808 / Symmetry type: POINT |