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- EMDB-12221: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c... -

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Entry
Database: EMDB / ID: EMD-12221
TitleVPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex
Map dataSharpened, locally filtered map of VPS26 dimer region of the metazoan retromer:SNX3 assembled on the membrane
Sample
  • Complex: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex
    • Protein or peptide: Vacuolar protein sorting-associated protein 26A
    • Protein or peptide: Sorting nexin-3
    • Protein or peptide: C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)
    • Protein or peptide: Vacuolar protein sorting-associated protein 35
  • Ligand: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
Keywordsendosomes / coat proteins / membrane trafficking / cargo-sorting / ENDOCYTOSIS
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 / inorganic cation transmembrane transporter activity / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / cadmium ion transmembrane transport / Metal ion SLC transporters / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / manganese ion transport / nickel cation transport / mitochondrion to lysosome vesicle-mediated transport / detection of oxygen / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / intralumenal vesicle formation / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / positive regulation of locomotion involved in locomotory behavior / iron import into cell / negative regulation of lysosomal protein catabolic process / copper ion transmembrane transporter activity / cobalt ion transport / cobalt ion transmembrane transporter activity / negative regulation of late endosome to lysosome transport / retromer complex binding / vesicle-mediated transport in synapse / positive regulation of dopamine biosynthetic process / mitochondrial fragmentation involved in apoptotic process / positive regulation of dopamine receptor signaling pathway / ferrous iron transmembrane transporter activity / phosphatidylinositol-5-phosphate binding / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to endosome / iron ion transmembrane transporter activity / retromer complex / zinc ion transmembrane transporter activity / voluntary musculoskeletal movement / iron ion transmembrane transport / copper ion transport / host-mediated suppression of symbiont invasion / basal part of cell / dopaminergic synapse / regulation of protein metabolic process / transcytosis / regulation of synapse maturation / endocytic recycling / early phagosome / phosphatidylinositol-3-phosphate binding / vacuole / regulation of Wnt signaling pathway / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / regulation of mitochondrion organization / response to iron ion / positive regulation of protein localization to cell periphery / clathrin-coated vesicle / heme biosynthetic process / dendrite morphogenesis / lysosome organization / negative regulation of phagocytosis / positive regulation of mitochondrial fission / cadmium ion binding / regulation of postsynapse assembly / regulation of presynapse assembly / regulation of macroautophagy / D1 dopamine receptor binding / erythrocyte development / intracellular protein transport / response to bacterium / trans-Golgi network / modulation of chemical synaptic transmission / Iron uptake and transport / brush border membrane / protein destabilization / regulation of protein stability / negative regulation of protein catabolic process / recycling endosome / positive regulation of neuron projection development / multicellular organismal-level iron ion homeostasis / negative regulation of inflammatory response / Wnt signaling pathway / 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 / 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
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 speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 9.5 Å
AuthorsLeneva N / Kovtun O
Funding support United Kingdom, 5 items
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, 2021-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0995
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0995
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7blo
  • Surface level: 0.0995
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12221.png

Downloads & links

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Map

FileDownload / File: emd_12221.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened, locally filtered map of VPS26 dimer region of the metazoan retromer:SNX3 assembled on the membrane
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 168 pix.
= 285.768 Å		1.7 Å/pix.
x 168 pix.
= 285.768 Å		1.7 Å/pix.
x 168 pix.
= 285.768 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.701 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0995 / Movie #1: 0.0995
Minimum - Maximum-0.24752396 - 0.47768217
Average (Standard dev.)0.0017648037 (±0.026295396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 285.768 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7011.7011.701
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z285.768285.768285.768
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.2480.4780.002

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Supplemental data

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Mask #1

Fileemd_12221_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map1

Fileemd_12221_half_map_1.map
Annotationhalf-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map2

Fileemd_12221_half_map_2.map
Annotationhalf-map2
Projections & Slices
AxesZYX

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Sample components

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Entire : VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c...

EntireName: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex
Components
  • Complex: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex
    • Protein or peptide: Vacuolar protein sorting-associated protein 26A
    • Protein or peptide: Sorting nexin-3
    • Protein or peptide: C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)
    • Protein or peptide: Vacuolar protein sorting-associated protein 35
  • Ligand: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE

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Supramolecule #1: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c...

SupramoleculeName: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide.
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Vacuolar protein sorting-associated protein 26A

MacromoleculeName: Vacuolar protein sorting-associated protein 26A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.364617 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FGPICEIDIV LNDGETRKMA EMKTEDGKVE KHYLFYDGES VSGKVNLAFK QPGKRLEHQG IRIEFVGQIE LFNDKSNTHE FVNLVKELA LPGELTQSRS YDFEFMQVEK PYESYIGANV RLRYFLKVTI VRRLTDLVKE YDLIVHQLAT YPDVNNSIKM E VGIEDCLH ...String:
FGPICEIDIV LNDGETRKMA EMKTEDGKVE KHYLFYDGES VSGKVNLAFK QPGKRLEHQG IRIEFVGQIE LFNDKSNTHE FVNLVKELA LPGELTQSRS YDFEFMQVEK PYESYIGANV RLRYFLKVTI VRRLTDLVKE YDLIVHQLAT YPDVNNSIKM E VGIEDCLH IEFEYNKSKY HLKDVIVGKI YFLLVRIKIQ HMELQLIKKE ITGIGPSTTT ETETIAKYEI MDGAPVKGES IP IRLFLAG YDPTPTMRDV NKKFSVRYFL NLVLVDEEDR RYFKQQEIIL WRKAPEK

UniProtKB: Vacuolar protein sorting-associated protein 26A

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Macromolecule #2: Sorting nexin-3

MacromoleculeName: Sorting nexin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 17.979393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TVADTRRLIT KPQNLNDAYG PPSNFLEIDV SNPQTVGVGR GRFTTYEIRV KTNLPIFKLK ESTVRRRYSD FEWLRSELER ESKVVVPPL PGKAFLRQLP FRGDDGIFDD NFIEERKQGL EQFINKVAGH PLAQNERCLH MFLQDEIIDK SYTPSK

UniProtKB: Sorting nexin-3

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Macromolecule #3: C-term (residues 493-54) of Wls (fitted sequence corresponds to h...

MacromoleculeName: C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II)
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 1.221422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QPELYLLNTM

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Macromolecule #4: Vacuolar protein sorting-associated protein 35

MacromoleculeName: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.714016 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QEKLLDEAIQ AVKVQSFQMK RCLDKNKLMD ALKHASNMLG ELRTSMLSPK SYYELYMAIS DELHYLEVYL TDEFAKGRKV ADLYELVQY AGNIIPRLYL LITVGVVYVK SFPQSRKDIL KDLVEMCRGV QHPLRGLFLR NYLLQCTRNI LPDEGEPTDE E TTGDISDS ...String:
QEKLLDEAIQ AVKVQSFQMK RCLDKNKLMD ALKHASNMLG ELRTSMLSPK SYYELYMAIS DELHYLEVYL TDEFAKGRKV ADLYELVQY AGNIIPRLYL LITVGVVYVK SFPQSRKDIL KDLVEMCRGV QHPLRGLFLR NYLLQCTRNI LPDEGEPTDE E TTGDISDS MDFVLLNFAE MNKLWVRMQH QGHSRDREKR ERERQELRIL VGTNLVRLSQ LEGVNVERYK QIVLTGILEQ VV NCRDALA QEYLMECIIQ VFPDEFHLQT LNPFLRACAE LHQNVNVKNI IIALIDRLAL FAHREDGPGI PADIKLFDIF SQQ VATVIQ SRQDMPSEDV VSLQVSLINL AMKCYP

UniProtKB: Vacuolar protein sorting-associated protein 35

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Macromolecule #5: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOX...

MacromoleculeName: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
type: ligand / ID: 5 / Number of copies: 2 / Formula: PIB
Molecular weightTheoretical: 554.374 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 66271
ExtractionNumber tomograms: 113 / Number images used: 822112
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5f0l


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7blo:
VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins

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