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- EMDB-75745: RNA Vault extended conformation (MVP/PARP4/TEP1 sample) -

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Basic information

Entry
Database: EMDB / ID: EMD-75745
TitleRNA Vault extended conformation (MVP/PARP4/TEP1 sample)
Map data
Sample
  • Complex: RNA Vault with ADPR bound (MVP/PARP4/TEP1 sample)
    • Protein or peptide: Major Vault Protein
KeywordsRNA Vault / complex / TEP1 / PARP4 / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 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_75745.png

Downloads & links

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Map

FileDownload / File: emd_75745.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: 0.16
Minimum - Maximum-1.0137423 - 1.8597244
Average (Standard dev.)0.0011518849 (±0.053027324)
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_75745_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: #1

Fileemd_75745_additional_1.map
Projections & Slices
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Half map: #1

Fileemd_75745_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_75745_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 with ADPR bound (MVP/PARP4/TEP1 sample)

EntireName: RNA Vault with ADPR bound (MVP/PARP4/TEP1 sample)
Components
  • Complex: RNA Vault with ADPR bound (MVP/PARP4/TEP1 sample)
    • Protein or peptide: Major Vault Protein

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Supramolecule #1: RNA Vault with ADPR bound (MVP/PARP4/TEP1 sample)

SupramoleculeName: RNA Vault with ADPR bound (MVP/PARP4/TEP1 sample) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Major Vault Protein

MacromoleculeName: Major Vault Protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATEEFIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPMRM VTVPPRHYCT VANPVSRDAQ GLVLFDVTGQ VRLRHADLEI RLAQDPFPLY PGEVLEKDIT PLQVVLPNTA LHLKALLDFE DKDGDKVVAG DEWLFEGPGT YIPRKEVEVV EIIQATIIRQ ...String:
MATEEFIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPMRM VTVPPRHYCT VANPVSRDAQ GLVLFDVTGQ VRLRHADLEI RLAQDPFPLY PGEVLEKDIT PLQVVLPNTA LHLKALLDFE DKDGDKVVAG DEWLFEGPGT YIPRKEVEVV EIIQATIIRQ NQALRLRARK ECWDRDGKER VTGEEWLVTT VGAYLPAVFE EVLDLVDAVI LTEKTALHLR ARRNFRDFRG VSRRTGEEWL VTVQDTEAHV PDVHEEVLGV VPITTLGPHN YCVILDPVGP DGKNQLGQKR VVKGEKSFFL QPGEQLEQGI QDVYVLSEQQ GLLLRALQPL EEGEDEEKVS HQAGDHWLIR GPLEYVPSAK VEVVEERQAI PLDENEGIYV QDVKTGKVRA VIGSTYMLTQ DEVLWEKELP PGVEELLNKG QDPLADRGEK DTAKSLQPLA PRNKTRVVSY RVPHNAAVQV YDYREKRARV VFGPELVSLG PEEQFTVLSL SAGRPKRPHA RRALCLLLGP DFFTDVITIE TADHARLQLQ LAYNWHFEVN DRKDPQETAK LFSVPDFVGD ACKAIASRVR GAVASVTFDD FHKNSARIIR TAVFGFETSE AKGPDGMALP RPRDQAVFPQ NGLVVSSVDV QSVEPVDQRT RDALQRSVQL AIEITTNSQE AAAKHEAQRL EQEARGRLER QKILDQSEAE KARKELLELE ALSMAVESTG TAKAEAESRA EAARIEGEGS VLQAKLKAQA LAIETEAELQ RVQKVRELEL VYARAQLELE VSKAQQLAEV EVKKFKQMTE AIGPSTIRDL AVAGPEMQVK LLQSLGLKST LITDGSTPIN LFNTAFGLLG MGPEGQPLGR RVASGPSPGE GISPQSAQAP QAPGDNHVVP VLR

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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: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 36446
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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