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- PDB-7blq: Vps26 dimer region of the fungal membrane-assembled retromer:Grd1... -

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Basic information

Entry
Database: PDB / ID: 7blq
TitleVps26 dimer region of the fungal membrane-assembled retromer:Grd19 complex.
Components
  • Sorting nexin-3
  • The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.
  • Vacuolar protein sorting-associated protein 26-like protein
  • Vacuolar protein sorting-associated protein 35
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 / lead ion transport / nickel cation transmembrane transporter activity / cadmium ion transmembrane transport / nickel cation 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 / lead ion transport / nickel cation transmembrane transporter activity / cadmium ion transmembrane transport / nickel cation transport / solute:proton symporter activity / inorganic cation transmembrane transporter activity / Metal ion SLC transporters / detection of oxygen / iron ion transmembrane transporter activity / zinc ion transmembrane transporter activity / manganese ion transport / iron ion transmembrane transport / manganese ion transmembrane transporter activity / cobalt ion transport / retromer, cargo-selective complex / cadmium ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / iron import into cell / retromer complex binding / copper ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / retromer complex / copper ion transport / basal part of cell / phosphatidylinositol-3-phosphate binding / retrograde transport, endosome to Golgi / response to iron ion / vacuole / dendrite morphogenesis / heme biosynthetic process / cadmium ion binding / erythrocyte development / brush border membrane / Iron uptake and transport / intracellular protein transport / trans-Golgi network / recycling endosome / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / extracellular vesicle / late endosome / apical part of cell / late endosome membrane / iron ion transport / early endosome membrane / cellular response to oxidative stress / cytoplasmic vesicle / intracellular iron ion homeostasis / mitochondrial outer membrane / learning or memory / lysosome / early endosome / endosome membrane / response to hypoxia / endosome / apical plasma membrane / lysosomal membrane / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / mitochondrion / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Fungal 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. ...Fungal 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
Similarity search - Domain/homology
Chem-PIB / Vacuolar protein sorting-associated protein 26-like protein / Sorting nexin-3 / Vacuolar protein sorting-associated protein 35 / Natural resistance-associated macrophage protein 2
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 9.2 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
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

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Structure visualization

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Assembly

Deposited unit
C: Vacuolar protein sorting-associated protein 35
A: Vacuolar protein sorting-associated protein 35
G: Sorting nexin-3
J: Vacuolar protein sorting-associated protein 26-like protein
F: Vacuolar protein sorting-associated protein 26-like protein
L: Sorting nexin-3
V: The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.
U: The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,24810
Polymers166,1398
Non-polymers1,1092
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8100 Å2
ΔGint-38 kcal/mol
Surface area73130 Å2
MethodPISA

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Components

#1: Protein Vacuolar protein sorting-associated protein 35


Mass: 34014.195 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 Sorting nexin-3


Mass: 13525.490 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_0011560 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0X3
#3: Protein Vacuolar protein sorting-associated protein 26-like protein


Mass: 34308.449 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_0009750 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S0E6
#4: Protein/peptide The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.


Mass: 1221.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Production host: Escherichia coli (E. coli) / References: UniProt: P49281*PLUS
#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 the fungal membrane-assembled retromer:Grd19 cargo-containing complex
Type: COMPLEX
Details: fungal retromer:Grd19 complex assembled on liposomes containing Kex2 cargo peptide.
Entity ID: #1-#4 / 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 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49886 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 82 / Num. of volumes extracted: 449807

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