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- PDB-7blo: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c... -

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Basic information

Entry
Database: PDB / ID: 7blo
TitleVPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins
Components
  • C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)
  • Sorting nexin-3
  • Vacuolar protein sorting-associated protein 26A
  • Vacuolar protein sorting-associated protein 35
KeywordsENDOCYTOSIS / endosomes / coat proteins / membrane trafficking / cargo-sorting
Function / homology
Function and homology information


negative regulation of early endosome to late endosome transport / vanadium ion transmembrane transporter activity / vanadium ion transport / 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 / transition metal ion transmembrane transporter activity / late endosome to Golgi transport ...negative regulation of early endosome to late endosome transport / vanadium ion transmembrane transporter activity / vanadium ion transport / 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 / transition metal ion transmembrane transporter activity / late endosome to Golgi transport / negative regulation of protein transport / protein to membrane docking / neurotransmitter receptor transport, endosome to plasma membrane / solute:proton symporter activity / membrane invagination / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / : / cadmium ion transmembrane transport / negative regulation of protein homooligomerization / tubular endosome / Metal ion SLC transporters / regulation of terminal button organization / positive regulation of Wnt protein secretion / nickel cation transport / manganese ion transport / WNT ligand biogenesis and trafficking / detection of oxygen / retromer, cargo-selective complex / mitochondrion to lysosome vesicle-mediated transport / intralumenal vesicle formation / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / copper ion transmembrane transporter activity / negative regulation of lysosomal protein catabolic process / positive regulation of locomotion involved in locomotory behavior / iron import into cell / cobalt ion transport / cobalt ion transmembrane transporter activity / negative regulation of late endosome to lysosome transport / retromer complex binding / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / ferrous iron transmembrane transporter activity / phosphatidylinositol-5-phosphate binding / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / iron ion transmembrane transporter activity / retromer complex / vesicle-mediated transport in synapse / zinc ion transmembrane transporter activity / voluntary musculoskeletal movement / mitochondrial fragmentation involved in apoptotic process / iron ion transmembrane transport / transcytosis / copper ion transport / host-mediated suppression of symbiont invasion / basal part of cell / regulation of protein metabolic process / dopaminergic synapse / early phagosome / regulation of synapse maturation / phosphatidylinositol-3-phosphate binding / endocytic recycling / vacuole / phosphatidylinositol-4-phosphate binding / regulation of mitochondrion organization / regulation of Wnt signaling pathway / retrograde transport, endosome to Golgi / phosphatidylinositol-3,5-bisphosphate binding / response to iron ion / clathrin-coated vesicle / heme biosynthetic process / positive regulation of protein localization to cell periphery / negative regulation of phagocytosis / lysosome organization / positive regulation of mitochondrial fission / dendrite morphogenesis / erythrocyte development / cadmium ion binding / regulation of postsynapse assembly / regulation of macroautophagy / regulation of presynapse assembly / D1 dopamine receptor binding / response to bacterium / intracellular protein transport / trans-Golgi network / brush border membrane / iron ion transport / Iron uptake and transport / positive regulation of neuron projection development / recycling endosome / protein destabilization / modulation of chemical synaptic transmission / negative regulation of protein catabolic process / regulation of protein stability / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / Wnt signaling pathway
Similarity search - Function
Vertebrate SNX3, PX domain / : / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / NRAMP family / Natural resistance-associated macrophage protein-like / PhoX homologous domain, present in p47phox and p40phox. ...Vertebrate SNX3, PX domain / : / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / NRAMP family / Natural resistance-associated macrophage protein-like / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Arrestin-like, C-terminal / Armadillo-type fold
Similarity search - Domain/homology
Chem-PIB / Sorting nexin-3 / Vacuolar protein sorting-associated protein 26A / Natural resistance-associated macrophage protein 2 / Sorting nexin-3 / Vacuolar protein sorting-associated protein 35
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.5 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 1.0Mar 3, 2021Provider: repository / Type: Initial release
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Revision 1.1Apr 7, 2021Group: Database references / Category: citation
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Revision 1.2Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model
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Structure visualization

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Assembly

Deposited unit
J: Vacuolar protein sorting-associated protein 26A
L: Sorting nexin-3
N: C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)
F: Vacuolar protein sorting-associated protein 26A
G: Sorting nexin-3
H: C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)
A: Vacuolar protein sorting-associated protein 35
C: Vacuolar protein sorting-associated protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,66810
Polymers188,5598
Non-polymers1,1092
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15450 Å2
ΔGint-67 kcal/mol
Surface area81220 Å2
MethodPISA

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Components

#1: Protein Vacuolar protein sorting-associated protein 26A / Vesicle protein sorting 26A / hVPS26


Mass: 34364.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VPS26A, VPS26 / Production host: Escherichia coli (E. coli) / References: UniProt: O75436
#2: Protein Sorting nexin-3


Mass: 17979.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Snx3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q78ZM0, UniProt: O60493*PLUS
#3: Protein/peptide C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)


Mass: 1221.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P49281*PLUS
#4: Protein Vacuolar protein sorting-associated protein 35 / hVPS35 / Maternal-embryonic 3 / Vesicle protein sorting 35


Mass: 40714.016 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
#5: Chemical ChemComp-PIB / 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE / D-MYO-PHOSPHATIDYLINOSITOL 3-PHOSPHATED (+)-SN-1,2-DI-O-BUTANOYLGLYCERYL,3-O-PHOSPHO


Mass: 554.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32O16P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex
Type: COMPLEX
Details: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide.
Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
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: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66271 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 113 / Num. of volumes extracted: 822112
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15F0L

5f0l

15F0L1PDBexperimental model
21

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