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- PDB-7bln: VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 com... -

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Basic information

Entry
Database: PDB / ID: 7bln
TitleVPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins
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


neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / WNT ligand biogenesis and trafficking ...neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / positive regulation of locomotion involved in locomotory behavior / negative regulation of lysosomal protein catabolic process / negative regulation of late endosome to lysosome transport / vesicle-mediated transport in synapse / positive regulation of dopamine biosynthetic process / mitochondrial fragmentation involved in apoptotic process / positive regulation of dopamine receptor signaling pathway / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / retromer complex / voluntary musculoskeletal movement / dopaminergic synapse / regulation of protein metabolic process / transcytosis / regulation of synapse maturation / endocytic recycling / retrograde transport, endosome to Golgi / regulation of mitochondrion organization / positive regulation of protein localization to cell periphery / lysosome organization / positive regulation of mitochondrial fission / regulation of postsynapse assembly / regulation of presynapse assembly / regulation of macroautophagy / D1 dopamine receptor binding / intracellular protein transport / modulation of chemical synaptic transmission / protein destabilization / regulation of protein stability / negative regulation of inflammatory response / Wnt signaling pathway / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / presynapse / early endosome / lysosome / neuron projection / postsynaptic density / endosome / endosome membrane / lysosomal membrane / negative regulation of gene expression / neuronal cell body / intracellular membrane-bounded organelle / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / metal ion binding / 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 / Armadillo-type fold
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 8.9 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 1.1Apr 7, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)224,6974
Polymers224,6974
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4380 Å2
ΔGint-22 kcal/mol
Surface area94110 Å2

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Components

#1: Protein Vacuolar protein sorting-associated protein 29 / hVPS29 / PEP11 homolog / Vesicle protein sorting 29


Mass: 20531.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS29, DC15, DC7, MDS007 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UBQ0
#2: Protein Vacuolar protein sorting-associated protein 35 / hVPS35 / Maternal-embryonic 3 / Vesicle protein sorting 35


Mass: 91816.805 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

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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 metazoan retromer:SNX3 complex.
Type: COMPLEX
Details: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide.
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
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 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 89313 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 113 / Num. of volumes extracted: 822112
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-ID
12R17

2r17

A2R171
25F0L

5f0l

A5F0L2
32R17

2r17

B2R171

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