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- EMDB-56516: In situ Dictyostelium discoideum cytosolic vault -

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Basic information

Entry
Database: EMDB / ID: EMD-56516
TitleIn situ Dictyostelium discoideum cytosolic vault
Map dataIn situ Dictyostelium cytosolic vault (masked)
Sample
  • Cell: In situ Dictyostelium discoideum cytosolic vault
Keywordsvault / protein cage / SPFH / STRUCTURAL PROTEIN
Biological speciesDictyostelium discoideum AX2 (eukaryote)
Methodsubtomogram averaging / cryo EM / Resolution: 29.0 Å
AuthorsGeissler K / Kreysing JP / Beck M
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2026
Title: The vault associates with membranes in situ.
Authors: Katharina Geißler / Jan Philipp Kreysing / Yuning Wang / Desislava Glushkova / Agnieszka Obarska-Kosinska / Patrick C Hoffmann / Stefanie Böhm / Alexander Schmidt / Jakob Meier-Credo / ...Authors: Katharina Geißler / Jan Philipp Kreysing / Yuning Wang / Desislava Glushkova / Agnieszka Obarska-Kosinska / Patrick C Hoffmann / Stefanie Böhm / Alexander Schmidt / Jakob Meier-Credo / Julian D Langer / Gerhard Hummer / Martin Beck /
Abstract: The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using ...The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using cryo-electron tomography of Dictyostelium discoideum cells, we define the distribution, structural states, and interaction landscape of vault particles in situ. Surprisingly, we detect a subpopulation of vault particles associated with the endoplasmic reticulum (ER) and nuclear envelope membranes. This association occurs at a defined barrel height of the vault particle. Membrane-associated particles appear to localize to patches of reduced membrane bilayer thickness and altered curvature. We further find that a fraction of vaults encloses 80S ribosomes in highly ordered orientations. These structural findings are further corroborated by proximity labeling experiments, which identify ER-resident proteins and numerous ribosomal components as vault particle interactors. The membrane-bound and ribosome-encapsulating vault populations that we uncover will direct future studies towards revealing vault function.
History
DepositionJan 29, 2026-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56516.png

Downloads & links

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Map

FileDownload / File: emd_56516.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ Dictyostelium cytosolic vault (masked)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.7 Å/pix.
x 100 pix.
= 870.4 Å		8.7 Å/pix.
x 100 pix.
= 870.4 Å		8.7 Å/pix.
x 100 pix.
= 870.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.704 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.4179893 - 0.670004
Average (Standard dev.)0.00000030564394 (±0.053987656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 870.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: In situ Dictyostelium cytosolic vault halfmap 1

Fileemd_56516_half_map_1.map
AnnotationIn situ Dictyostelium cytosolic vault halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: In situ Dictyostelium cytosolic vault halfmap 2

Fileemd_56516_half_map_2.map
AnnotationIn situ Dictyostelium cytosolic vault halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In situ Dictyostelium discoideum cytosolic vault

EntireName: In situ Dictyostelium discoideum cytosolic vault
Components
  • Cell: In situ Dictyostelium discoideum cytosolic vault

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Supramolecule #1: In situ Dictyostelium discoideum cytosolic vault

SupramoleculeName: In situ Dictyostelium discoideum cytosolic vault / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Dictyostelium discoideum AX2 (eukaryote) / Strain: Ax2-214

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 6.5
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 42000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C39 (39 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 29.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: novaSTA / Number subtomograms used: 985
ExtractionNumber tomograms: 318 / Number images used: 985 / Software - Name: novaSTA
CTF correctionSoftware - Name: NOVACTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER / Software - Name: novaSTA / Details: Cross correlations
FSC plot (resolution estimation)

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