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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: Adam Osinski / Benjamin Mayro / Victor A Lopez / Jason Schrad / Hannah Choi / Diana R Tomchick / Krzysztof Pawłowski / Kevin Forsberg / Sarah H Shahmoradian / Vincent S Tagliabracci /
Abstract: Across all domains of life, organisms exploit NAD metabolism as a central line of defense against invading pathogens. Here, we show that domain of unknown function 4062 (DUF4062) is a widespread ...Across all domains of life, organisms exploit NAD metabolism as a central line of defense against invading pathogens. Here, we show that domain of unknown function 4062 (DUF4062) is a widespread family of TIR-like NADases that hydrolyze NAD to ADP-ribose and nicotinamide. In bacteria, DUF4062 homologs form a previously unrecognized antiphage defense system, which we name Swarożyc, that assembles with the phage portal into a supramolecular NADase complex to induce abortive infection. In eukaryotes, DUF4062 is found in TEP1, which we demonstrate functions as an active NADase within the RNA vault, an enigmatic organelle-like structure. Single-particle cryo-electron microscopy reveals ADP-ribose bound within the shoulder of both reconstituted and human brain vaults, while cryo-electron tomography positions TEP1 along the central axis at the shoulder. Thus, TEP1, like bacterial Swarożyc, functions by depleting NAD, providing new insight into the long-standing mystery of vault function.
History
DepositionFeb 27, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 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
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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

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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
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Additional map: #1

Fileemd_75745_additional_1.map
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Half map: #1

Fileemd_75745_half_map_1.map
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Half map: #2

Fileemd_75745_half_map_2.map
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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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