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- PDB-7bln: VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bln | ||||||||||||||||||
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Title | VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins | ||||||||||||||||||
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![]() | ENDOCYTOSIS / endosomes / coat proteins / membrane trafficking / cargo-sorting | ||||||||||||||||||
Function / homology | ![]() 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 ...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 / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / 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 / 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 / regulation of protein metabolic process / transcytosis / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / regulation of mitochondrion organization / positive regulation of mitochondrial fission / lysosome organization / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / intracellular protein transport / protein destabilization / modulation of chemical synaptic transmission / regulation of protein stability / Wnt signaling pathway / negative regulation of inflammatory response / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / presynapse / postsynaptic density / lysosome / early endosome / endosome membrane / endosome / neuron projection / lysosomal membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / perinuclear region of cytoplasm / extracellular exosome / metal ion binding / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.9 Å | ||||||||||||||||||
![]() | Leneva, N. / Kovtun, O. / Morado, D.R. / Briggs, J.A.G. / Owen, D.J. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly. Authors: Natalya Leneva / Oleksiy Kovtun / Dustin R Morado / John A G Briggs / David J Owen / ![]() Abstract: Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core ...Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes. | ||||||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 342.3 KB | Display | ![]() |
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PDB format | ![]() | 280.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 75.4 KB | Display | |
Data in CIF | ![]() | 111.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 12220MC ![]() 7bloC ![]() 7blpC ![]() 7blqC ![]() 7blrC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 764.9 Data #1: Raw image frames for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [micrographs - multiframe] Data #2: Corrected, aligned and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [tilt series] Data #3: Corrected, aligned, dose-filtered and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [tilt series]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 20531.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 91816.805 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging |
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Sample preparation
Component | Name: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex. Type: COMPLEX Details: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide. Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89313 / Symmetry type: POINT | ||||||||||||||||||||
EM volume selection | Num. of tomograms: 113 / Num. of volumes extracted: 822112 | ||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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