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- EMDB-75744: RNA Vault intermediate conformation (MVP/PARP4/TEP1 sample) -

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Basic information

Entry
Database: EMDB / ID: EMD-75744
TitleRNA Vault intermediate conformation (MVP/PARP4/TEP1 sample)
Map data
Sample
  • Complex: RNA Vault intermediate conformation (MVP/PARP4/TEP1 sample)
KeywordsRNA Vault / complex / TEP1 / PARP4 / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsOsinski A / Tagliabracci VS
Funding support United States, 5 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM137419 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158265 United States
Welch FoundationI-1911 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR150033 United States
CitationJournal: Biorxiv / Year: 2026
Title: TIR-like NADases act in bacterial immunity and the RNA vault
Authors: Osinski A / Mayro B / Lopez VA / Schrad J / Choi H / Tomchick DR / Pawlowski K / Forsberg K / Shahmoradian SH / Tagliabracci VS
History
DepositionFeb 27, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75744.png

Downloads & links

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Map

FileDownload / File: emd_75744.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 800 pix.
= 855.6 Å		1.07 Å/pix.
x 800 pix.
= 855.6 Å		1.07 Å/pix.
x 800 pix.
= 855.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0695 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.68211746 - 1.5521473
Average (Standard dev.)0.0016289856 (±0.048566498)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 855.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75744_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_75744_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75744_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75744_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RNA Vault intermediate conformation (MVP/PARP4/TEP1 sample)

EntireName: RNA Vault intermediate conformation (MVP/PARP4/TEP1 sample)
Components
  • Complex: RNA Vault intermediate conformation (MVP/PARP4/TEP1 sample)

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Supramolecule #1: RNA Vault intermediate conformation (MVP/PARP4/TEP1 sample)

SupramoleculeName: RNA Vault intermediate conformation (MVP/PARP4/TEP1 sample)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Details: 50 Tris 8.0, 75 mM NaCl, 1.5 mM MgCl2, 1 mM DTT, 1 mM NADP, 0.025% DDM
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D39 (2x39 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5897
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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