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Yorodumi- PDB-7blr: Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7blr | ||||||||||||||||||
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Title | Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-BAR) complex. | ||||||||||||||||||
Components |
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Keywords | ENDOCYTOSIS / endosomes / coat proteins / membrane trafficking / cargo-sorting | ||||||||||||||||||
Function / homology | Function and homology information retromer, cargo-selective complex / retromer complex / retrograde transport, endosome to Golgi / protein transport / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Chaetomium thermophilum (fungus) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.3 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 |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7blr.cif.gz | 339.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7blr.ent.gz | 271.3 KB | Display | PDB format |
PDBx/mmJSON format | 7blr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7blr_validation.pdf.gz | 983.3 KB | Display | wwPDB validaton report |
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Full document | 7blr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7blr_validation.xml.gz | 73.2 KB | Display | |
Data in CIF | 7blr_validation.cif.gz | 108.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/7blr ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7blr | HTTPS FTP |
-Related structure data
Related structure data | 12226MC 7blnC 7bloC 7blpC 7blqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 98566.781 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: 22330.602 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_0002370 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZB5 |
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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: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex. Type: COMPLEX Details: fungal retromer:Vps5 complex assembled on liposomes. Entity ID: all / 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: 3.17 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18680 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 71 / Num. of volumes extracted: 18680 | ||||||||||||||||||||||||
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