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- PDB-7blr: Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7blr | ||||||||||||||||||
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Title | Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-BAR) complex. | ||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||
![]() | 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
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 339.4 KB | Display | ![]() |
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PDB format | ![]() | 271.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12226MC ![]() 7blnC ![]() 7bloC ![]() 7blpC ![]() 7blqC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0035730 / Production host: ![]() ![]() ![]() #2: Protein | ![]() Mass: 22330.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0002370 / Production host: ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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 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: ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
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: 3.17 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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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![]() | ||||||||||||||||||||||||
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 | ||||||||||||||||||||||||
Refine LS restraints |
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