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- EMDB-19879: COPII coat on native membranes - 5-way vertex -

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Basic information

Entry
Database: EMDB / ID: EMD-19879
TitleCOPII coat on native membranes - 5-way vertex
Map dataCOPII on microsomes: Average of vertices formed by convergence of 5 rods
Sample
  • Complex: Sec13-Sec31
KeywordsCOPII / TRANSPORT PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsPyle E / Zanetti G
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes.
Authors: Euan Pyle / Elizabeth A Miller / Giulia Zanetti /
Abstract: Proteins traverse the eukaryotic secretory pathway through membrane trafficking between organelles. The coat protein complex II (COPII) mediates the anterograde transport of newly synthesized ...Proteins traverse the eukaryotic secretory pathway through membrane trafficking between organelles. The coat protein complex II (COPII) mediates the anterograde transport of newly synthesized proteins from the endoplasmic reticulum, engaging cargoes with a wide range of size and biophysical properties. The native architecture of the COPII coat and how cargo might influence COPII carrier morphology remain poorly understood. Here we reconstituted COPII-coated membrane carriers using purified Saccharomyces cerevisiae proteins and cell-derived microsomes as a native membrane source. Using cryo-electron tomography with subtomogram averaging, we demonstrate that the COPII coat binds cargo and forms largely spherical vesicles from native membranes. We reveal the architecture of the inner and outer coat layers and shed light on how spherical carriers are formed. Our results provide insights into the architecture and regulation of the COPII coat and advance our current understanding of how membrane curvature is generated.
History
DepositionMar 18, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19879.png

Downloads & links

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Map

FileDownload / File: emd_19879.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCOPII on microsomes: Average of vertices formed by convergence of 5 rods
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
12.21 Å/pix.
x 64 pix.
= 781.312 Å		12.21 Å/pix.
x 64 pix.
= 781.312 Å		12.21 Å/pix.
x 64 pix.
= 781.312 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 12.208 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.09284121 - 0.27431566
Average (Standard dev.)0.0036122885 (±0.046790935)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 781.312 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half 1

Fileemd_19879_half_map_1.map
Annotationhalf 1
Projections & Slices
AxesZYX

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Half map: half2

Fileemd_19879_half_map_2.map
Annotationhalf2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Sec13-Sec31

EntireName: Sec13-Sec31
Components
  • Complex: Sec13-Sec31

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Supramolecule #1: Sec13-Sec31

SupramoleculeName: Sec13-Sec31 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.005 µm / Nominal defocus min: 0.003 µm
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: 35.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 461
ExtractionNumber tomograms: 800 / Number images used: 461
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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