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

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Basic information

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 26AVacuole
    • 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 35Vacuole
  • Ligand: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
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
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 / Morado DR / Briggs JAG / Owen DJ
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 7, 2021-
Current statusApr 7, 2021Processing 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
Voxel sizeX=Y=Z: 1.701 Å
Density
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

Projections

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 26AVacuole
    • 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 35Vacuole
  • 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)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

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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

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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

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

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Image processing

ExtractionNumber tomograms: 113 / Number images used: 822112
Final angle assignmentType: OTHER
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
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5f0l

Output model

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

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