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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 26AVacuole
  • Vacuolar protein sorting-associated protein 35Vacuole
KeywordsENDOCYTOSIS / endosomes / coat proteins / membrane trafficking / cargo-sorting
Function / homology
Function and homology information


vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / nickel cation transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / cadmium ion transmembrane transport ...vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / nickel cation transmembrane transporter activity / lead ion transport / negative regulation of early endosome to late endosome transport / cadmium ion transmembrane transport / late endosome to Golgi transport / protein to membrane docking / nickel cation transport / negative regulation of protein transport / solute:proton symporter activity / positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of postsynapse assembly / inorganic cation transmembrane transporter activity / mitochondrion-derived vesicle / Metal ion SLC transporters / manganese ion transport / negative regulation of protein homooligomerization / membrane invagination / iron ion transmembrane transport / regulation of dendritic spine maintenance / manganese ion transmembrane transporter activity / zinc ion transmembrane transporter activity / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / detection of oxygen / positive regulation of Wnt protein secretion / iron ion transmembrane transporter activity / cadmium ion transmembrane transporter activity / regulation of terminal button organization / cobalt ion transport / retromer, cargo-selective complex / cobalt ion transmembrane transporter activity / vesicle-mediated transport in synapse / WNT ligand biogenesis and trafficking / intralumenal vesicle formation / iron import into cell / retromer complex binding / negative regulation of late endosome to lysosome transport / copper ion transmembrane transporter activity / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / ferrous iron transmembrane transporter activity / phosphatidylinositol-5-phosphate binding / dopaminergic synapse / mitochondrial fragmentation involved in apoptotic process / regulation of protein metabolic process / retromer complex / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / regulation of synapse maturation / voluntary musculoskeletal movement / copper ion transport / negative regulation of viral entry into host cell / basal part of cell / phosphatidylinositol-3-phosphate binding / transcytosis / endocytic recycling / early phagosome / positive regulation of protein localization to cell periphery / vacuole / phosphatidylinositol-4-phosphate binding / negative regulation of phagocytosis / retrograde transport, endosome to Golgi / phosphatidylinositol-3,5-bisphosphate binding / response to iron ion / regulation of mitochondrion organization / regulation of Wnt signaling pathway / dendrite morphogenesis / clathrin-coated vesicle / heme biosynthetic process / erythrocyte development / positive regulation of mitochondrial fission / lysosome organization / cadmium ion binding / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / brush border membrane / response to bacterium / Iron uptake and transport / intracellular protein transport / modulation of chemical synaptic transmission / protein destabilization / regulation of protein stability / trans-Golgi network / negative regulation of protein catabolic process / positive regulation of neuron projection development / recycling endosome / negative regulation of inflammatory response / Wnt signaling pathway / multicellular organismal-level iron ion homeostasis / recycling endosome membrane
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 / Arrestin-like, C-terminal / 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 / Arrestin-like, C-terminal / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 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
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

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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
Water0
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 / Vacuole / 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 / Vacuole / 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

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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 FIELDBright-field microscopy
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-ID
15F0L

5f0l

1
21

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