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Yorodumi- PDB-7blq: Vps26 dimer region of the fungal membrane-assembled retromer:Grd1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7blq | ||||||||||||||||||
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Title | Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 complex. | ||||||||||||||||||
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 / lead ion transport / nickel cation transmembrane transporter activity / cadmium ion transmembrane transport / nickel cation 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 / lead ion transport / nickel cation transmembrane transporter activity / cadmium ion transmembrane transport / nickel cation transport / solute:proton symporter activity / inorganic cation transmembrane transporter activity / Metal ion SLC transporters / zinc ion transmembrane transporter activity / manganese ion transport / detection of oxygen / cobalt ion transport / retromer, cargo-selective complex / cadmium ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron import into cell / iron ion transmembrane transporter activity / retromer complex binding / copper ion transmembrane transporter activity / iron ion transmembrane transport / ferrous iron transmembrane transporter activity / retromer complex / copper ion transport / basal part of cell / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi / response to iron ion / vacuole / dendrite morphogenesis / heme biosynthetic process / cadmium ion binding / erythrocyte development / brush border membrane / Iron uptake and transport / intracellular protein transport / trans-Golgi network / recycling endosome / activation of cysteine-type endopeptidase activity involved in apoptotic process / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / extracellular vesicle / late endosome / apical part of cell / early endosome membrane / late endosome membrane / iron ion transport / cellular response to oxidative stress / cytoplasmic vesicle / intracellular iron ion homeostasis / mitochondrial outer membrane / learning or memory / endosome / endosome membrane / early endosome / lysosome / response to hypoxia / apical plasma membrane / Golgi membrane / lysosomal membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / mitochondrion / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Chaetomium thermophilum (fungus) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.2 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 | 7blq.cif.gz | 264.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7blq.ent.gz | 213.2 KB | Display | PDB format |
PDBx/mmJSON format | 7blq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7blq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7blq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7blq_validation.xml.gz | 52 KB | Display | |
Data in CIF | 7blq_validation.cif.gz | 77 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/7blq ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7blq | HTTPS FTP |
-Related structure data
Related structure data | 12224MC 7blnC 7bloC 7blpC 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-10631 (Title: Cryo-electron tomography of the fungal membrane-assembled retromer:Grd19 coat containing Kex2 cargo motif Data size: 347.7 Data #1: Raw image frames for the fungal retromer:Grd19 coat assembled on the Kex2 cargo-containing membranes [micrographs - multiframe] Data #2: Corrected, aligned and order-sorted tilt series for the membrane-reconstituted fungal retromer:Grd19 complex in the presence of cargo-signal containing C-portion of the Kex2 cargo. [tilt series] Data #3: Corrected, aligned, dose-filtered and order-sorted tilt series for the membrane-reconstituted fungal retromer:Grd19 complex in the presence of cargo-signal containing C-portion of the Kex2 cargo. [tilt series]) |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 34014.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0035730 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S709 #2: Protein | Mass: 13525.490 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0011560 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0X3 #3: Protein | Mass: 34308.449 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0009750 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0E6 #4: Protein/peptide | Mass: 1221.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) Production host: Escherichia coli (E. coli) / References: UniProt: P49281*PLUS #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 the fungal membrane-assembled retromer:Grd19 cargo-containing complex Type: COMPLEX Details: fungal retromer:Grd19 complex assembled on liposomes containing Kex2 cargo peptide. Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
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 FIELD |
Image recording | Electron dose: 3 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C1 (asymmetric) |
3D reconstruction | Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49886 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 82 / Num. of volumes extracted: 449807 |