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- PDB-7blr: Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-... -

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Basic information

Entry
Database: PDB / ID: 7blr
TitleVps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-BAR) complex.
Components
  • Vacuolar protein sorting-associated protein 29
  • Vacuolar protein sorting-associated protein 35
KeywordsENDOCYTOSIS / endosomes / coat proteins / membrane trafficking / cargo-sorting
Function / homology
Function and homology information


retromer, cargo-selective complex / retromer complex / retrograde transport, endosome to Golgi / intracellular protein transport / late endosome / protein transport / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 29 / Vacuolar protein sorting-associated protein 35
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.3 Å
AuthorsLeneva, N. / Kovtun, O. / Morado, D.R. / Briggs, J.A.G. / Owen, D.J.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
Wellcome Trust207455/Z/17/Z United Kingdom
Wellcome Trust206171/Z/17/Z United Kingdom
Wellcome Trust202905/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSION United Kingdom
CitationJournal: 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
DepositionJan 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Feb 10, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Feb 10, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Feb 10, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
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Revision 1.1Apr 7, 2021Group: Database references / Category: citation
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Revision 1.2May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jul 9, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: Vacuolar protein sorting-associated protein 35
B: Vacuolar protein sorting-associated protein 29
C: Vacuolar protein sorting-associated protein 35
D: Vacuolar protein sorting-associated protein 29


Theoretical massNumber of molelcules
Total (without water)241,7954
Polymers241,7954
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6290 Å2
ΔGint-27 kcal/mol
Surface area90170 Å2
MethodPISA

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Components

#1: Protein Vacuolar protein sorting-associated protein 35


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 Vacuolar protein sorting-associated protein 29


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
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: 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
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 3.17 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18680 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 71 / Num. of volumes extracted: 18680
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01516762
ELECTRON MICROSCOPYf_angle_d1.00322748
ELECTRON MICROSCOPYf_dihedral_angle_d30.8292280
ELECTRON MICROSCOPYf_chiral_restr0.0492604
ELECTRON MICROSCOPYf_plane_restr0.0072952

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