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- EMDB-12225: tomogram of membrane tubules coated with fungal retromer:Grd19 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-12225
Titletomogram of membrane tubules coated with fungal retromer:Grd19 in the presence of Kex2 cargo.
Map datarepresentative tomogram of fungal retromer:Grd19:Kex2
Sample
  • Complex: membrane tubules coated with fungal retromer:Grd19 complex.
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Methodelectron tomography / cryo EM
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 31, 2021-
Map releaseMar 31, 2021-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_12225.png

Downloads & links

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Map

FileDownload / File: emd_12225.map.gz / Format: CCP4 / Size: 491.7 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
Annotationrepresentative tomogram of fungal retromer:Grd19:Kex2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.52 Å/pix.
x 300 pix.
= 1654.8 Å		5.52 Å/pix.
x 927 pix.
= 5113.332 Å		5.52 Å/pix.
x 927 pix.
= 5113.332 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 5.516 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-750.0 - 593.0
Average (Standard dev.)3.1675878e-05 (±93.7803)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions927927300
Spacing927927300
CellA: 5113.332 Å / B: 5113.332 Å / C: 1654.7999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z5.5165.5165.516
M x/y/z927927300
origin x/y/z0.0000.0000.000
length x/y/z5113.3325113.3321654.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS927927300
D min/max/mean-750.000593.0000.000

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Supplemental data

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Sample components

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Entire : membrane tubules coated with fungal retromer:Grd19 complex.

EntireName: membrane tubules coated with fungal retromer:Grd19 complex.
Components
  • Complex: membrane tubules coated with fungal retromer:Grd19 complex.

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Supramolecule #1: membrane tubules coated with fungal retromer:Grd19 complex.

SupramoleculeName: membrane tubules coated with fungal retromer:Grd19 complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: fungal retromer:Grd19 complex assembled on liposomes containing Kex2 cargo.
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation state3D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: BBI Solutions / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k 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 reconstructionNumber images used: 41

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