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Yorodumi- PDB-7blo: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c... -
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-Basic information
Entry | Database: PDB / ID: 7blo | ||||||||||||||||||
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Title | VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins | ||||||||||||||||||
Components |
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Keywords | ENDOCYTOSIS / endosomes / coat proteins / membrane trafficking / cargo-sorting | ||||||||||||||||||
Function / homology | Function and homology information vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / nickel cation transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / cadmium ion transmembrane transport ...vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / nickel cation transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / cadmium ion transmembrane transport / late endosome to Golgi transport / protein to membrane docking / nickel cation transport / solute:proton symporter activity / negative regulation of protein transport / positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / regulation of postsynapse assembly / inorganic cation transmembrane transporter activity / mitochondrion-derived vesicle / negative regulation of protein localization / Metal ion SLC transporters / membrane invagination / negative regulation of protein homooligomerization / manganese ion transport / iron ion transmembrane transport / regulation of dendritic spine maintenance / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / detection of oxygen / manganese ion transmembrane transporter activity / positive regulation of Wnt protein secretion / iron ion transmembrane transporter activity / zinc ion transmembrane transporter activity / regulation of terminal button organization / cadmium ion transmembrane transporter activity / cobalt ion transport / retromer, cargo-selective complex / cobalt ion transmembrane transporter activity / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / intralumenal vesicle formation / iron import into cell / retromer complex binding / negative regulation of late endosome to lysosome transport / copper ion transmembrane transporter activity / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / ferrous iron transmembrane transporter activity / mitochondrial fragmentation involved in apoptotic process / phosphatidylinositol-5-phosphate binding / retromer complex / protein localization to endosome / dopaminergic synapse / regulation of synapse maturation / neurotransmitter receptor transport, endosome to postsynaptic membrane / voluntary musculoskeletal movement / copper ion transport / negative regulation of viral entry into host cell / basal part of cell / regulation of protein metabolic process / phosphatidylinositol-3-phosphate binding / transcytosis / early phagosome / endocytic recycling / regulation of Wnt signaling pathway / positive regulation of protein localization to cell periphery / vacuole / retrograde transport, endosome to Golgi / regulation of mitochondrion organization / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to iron ion / negative regulation of phagocytosis / dendrite morphogenesis / clathrin-coated vesicle / heme biosynthetic process / positive regulation of mitochondrial fission / lysosome organization / cadmium ion binding / erythrocyte development / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / brush border membrane / Iron uptake and transport / intracellular protein transport / response to bacterium / protein destabilization / modulation of chemical synaptic transmission / trans-Golgi network / regulation of protein stability / negative regulation of protein catabolic process / recycling endosome / Wnt signaling pathway / multicellular organismal-level iron ion homeostasis / positive regulation of neuron projection development / negative regulation of inflammatory response / recycling endosome membrane Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.5 Å | ||||||||||||||||||
Authors | Leneva, N. / Kovtun, O. / Morado, D.R. / Briggs, J.A.G. / Owen, D.J. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Sci Adv / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7blo.cif.gz | 311.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7blo.ent.gz | 260.2 KB | Display | PDB format |
PDBx/mmJSON format | 7blo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/7blo ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7blo | HTTPS FTP |
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-Related structure data
Related structure data | 12221MC 7blnC 7blpC 7blqC 7blrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10633 (Title: Cryo-electron tomography of the metazoan membrane-assembled retromer:SNX3 coat containing Wls cargo motif 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]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 34364.617 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS26A, VPS26 / Production host: Escherichia coli (E. coli) / References: UniProt: O75436 #2: Protein | Mass: 17979.393 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q78ZM0, UniProt: O60493*PLUS #3: Protein/peptide | Mass: 1221.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P49281*PLUS #4: Protein | Mass: 40714.016 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VPS35, MEM3, TCCCTA00141 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QK1 #5: Chemical | Has ligand of interest | Y | |
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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 |
-Sample preparation
Component | Name: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex Type: COMPLEX Details: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide. Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
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 FIELDBright-field microscopy |
Image recording | Electron dose: 3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||
3D reconstruction | Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66271 / Symmetry type: POINT | |||||||||
EM volume selection | Num. of tomograms: 113 / Num. of volumes extracted: 822112 | |||||||||
Atomic model building |
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