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- EMDB-75735: RNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1... -

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Basic information

Entry
Database: EMDB / ID: EMD-75735
TitleRNA Vault bound to PARP4 MINT, focused refinement (MVP/PARP4/TEP1 NADP sample)
Map data
Sample
  • Complex: RNA Vault with ADPR bound (MVP/PARP4/TEP1 sample)
    • Protein or peptide: Major vault protein
  • Protein or peptide: Protein mono-ADP-ribosyltransferase PARP4
  • Ligand: water
KeywordsRNA Vault / complex / TEP1 / PARP4 / STRUCTURAL PROTEIN
Function / homology
Function and homology information


protein activation cascade / Maturation of nucleoprotein / Nicotinate metabolism / ERBB signaling pathway / Maturation of nucleoprotein / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of epidermal growth factor receptor signaling pathway ...protein activation cascade / Maturation of nucleoprotein / Nicotinate metabolism / ERBB signaling pathway / Maturation of nucleoprotein / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / negative regulation of epidermal growth factor receptor signaling pathway / NAD+ poly-ADP-ribosyltransferase activity / nuclear pore / mRNA transport / nucleotidyltransferase activity / protein modification process / spindle microtubule / protein transport / secretory granule lumen / protein phosphatase binding / ficolin-1-rich granule lumen / cytoskeleton / cell population proliferation / intracellular signal transduction / response to xenobiotic stimulus / ribonucleoprotein complex / inflammatory response / DNA repair / DNA damage response / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein mono-ADP-ribosyltransferase PARP4 / : / : / PARP4 MVP-ID C-terminal domain / PARP4 WGR-like domain / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / Major vault protein, N-terminal ...Protein mono-ADP-ribosyltransferase PARP4 / : / : / PARP4 MVP-ID C-terminal domain / PARP4 WGR-like domain / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain / Shoulder domain / Major Vault Protein repeat domain / Major Vault Protein Repeat domain / Major Vault Protein repeat domain / MVP (vault) repeat profile. / Band 7/SPFH domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / von Willebrand factor type A domain / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Major vault protein / Protein mono-ADP-ribosyltransferase PARP4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 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 26, 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_75735.png

Downloads & links

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Map

FileDownload / File: emd_75735.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 256 pix.
= 182.528 Å		0.71 Å/pix.
x 256 pix.
= 182.528 Å		0.71 Å/pix.
x 256 pix.
= 182.528 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.713 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.042
Minimum - Maximum-0.19672382 - 0.3164283
Average (Standard dev.)0.0015303433 (±0.01323839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 182.528 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_75735_msk_1.map
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Additional map: #1

Fileemd_75735_additional_1.map
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Half map: #1

Fileemd_75735_half_map_1.map
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Half map: #2

Fileemd_75735_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
  • Protein or peptide: Protein mono-ADP-ribosyltransferase PARP4
  • Ligand: water

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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: #1
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 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.452766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATEEFIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPMRM VTVPPRHYCT VANPVSRDAQ GLVLFDVTGQ VRLRHADLE IRLAQDPFPL YPGEVLEKDI TPLQVVLPNT ALHLKALLDF EDKDGDKVVA GDEWLFEGPG TYIPRKEVEV V EIIQATII ...String:
MATEEFIIRI PPYHYIHVLD QNSNVSRVEV GPKTYIRQDN ERVLFAPMRM VTVPPRHYCT VANPVSRDAQ GLVLFDVTGQ VRLRHADLE IRLAQDPFPL YPGEVLEKDI TPLQVVLPNT ALHLKALLDF EDKDGDKVVA GDEWLFEGPG TYIPRKEVEV V EIIQATII RQNQALRLRA RKECWDRDGK ERVTGEEWLV TTVGAYLPAV FEEVLDLVDA VILTEKTALH LRARRNFRDF RG VSRRTGE EWLVTVQDTE AHVPDVHEEV LGVVPITTLG PHNYCVILDP VGPDGKNQLG QKRVVKGEKS FFLQPGEQLE QGI QDVYVL SEQQGLLLRA LQPLEEGEDE EKVSHQAGDH WLIRGPLEYV PSAKVEVVEE RQAIPLDENE GIYVQDVKTG KVRA VIGST YMLTQDEVLW EKELPPGVEE LLNKGQDPLA DRGEKDTAKS LQPLAPRNKT RVVSYRVPHN AAVQVYDYRE KRARV VFGP ELVSLGPEEQ FTVLSLSAGR PKRPHARRAL CLLLGPDFFT DVITIETADH ARLQLQLAYN WHFEVNDRKD PQETAK LFS VPDFVGDACK AIASRVRGAV ASVTFDDFHK NSARIIRTAV FGFETSEAKG PDGMALPRPR DQAVFPQNGL VVSSVDV QS VEPVDQRTRD ALQRSVQLAI EITTNSQEAA AKHEAQRLEQ EARGRLERQK ILDQSEAEKA RKELLELEAL SMAVESTG T AKAEAESRAE AARIEGEGSV LQAKLKAQAL AIETEAELQR VQKVRELELV YARAQLELEV SKAQQLAEVE VKKFKQMTE AIGPSTIRDL AVAGPEMQVK LLQSLGLKST LITDGSTPIN LFNTAFGLLG MGPEGQPLGR RVASGPSPGE GISPQSAQAP QAPGDNHVV PVLR

UniProtKB: Major vault protein

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Macromolecule #2: Protein mono-ADP-ribosyltransferase PARP4

MacromoleculeName: Protein mono-ADP-ribosyltransferase PARP4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Pentosyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 192.810172 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVMGIFANCI FCLKVKYLPQ QQKKKLQTDI KENGGKFSFS LNPQCTHIIL DNADVLSQYQ LNSIQKNHVH IANPDFIWKS IREKRLLDV KNYDPYKPLD ITPPPDQKAS SSEVKTEGLC PDSATEEEDT VELTEFGMQN VEIPHLPQDF EVAKYNTLEK V GMEGGQEA ...String:
MVMGIFANCI FCLKVKYLPQ QQKKKLQTDI KENGGKFSFS LNPQCTHIIL DNADVLSQYQ LNSIQKNHVH IANPDFIWKS IREKRLLDV KNYDPYKPLD ITPPPDQKAS SSEVKTEGLC PDSATEEEDT VELTEFGMQN VEIPHLPQDF EVAKYNTLEK V GMEGGQEA VVVELQCSRD SRDCPFLISS HFLLDDGMET RRQFAIKKTS EDASEYFENY IEELKKQGFL LREHFTPEAT QL ASEQLQA LLLEEVMNSS TLSQEVSDLV EMIWAEALGH LEHMLLKPVN RISLNDVSKA EGILLLVKAA LKNGETAEQL QKM MTEFYR LIPHKGTMPK EVNLGLLAKK ADLCQLIRDM VNVCETNLSK PNPPSLAKYR ALRCKIEHVE QNTEEFLRVR KEVL QNHHS KSPVDVLQIF RVGRVNETTE FLSKLGNVRP LLHGSPVQNI VGILCRGLLL PKVVEDRGVQ RTDVGNLGSG IYFSD SLST SIKYSHPGET DGTRLLLICD VALGKCMDLH EKDFSLTEAP PGYDSVHGVS QTASVTTDFE DDEFVVYKTN QVKMKY IIK FSMPGDQIKD FHPSDHTELE EYRPEFSNFS KVEDYQLPDA KTSSSTKAGL QDASGNLVPL EDVHIKGRII DTVAQVI VF QTYTNKSHVP IEAKYIFPLD DKAAVCGFEA FINGKHIVGE IKEKEEAQQE YLEAVTQGHG AYLMSQDAPD VFTVSVGN L PPKAKVLIKI TYITELSILG TVGVFFMPAT VAPWQQDKAL NENLQDTVEK ICIKEIGTKQ SFSLTMSIEM PYVIEFIFS DTHELKQKRT DCKAVISTME GSSLDSSGFS LHIGLSAAYL PRMWVEKHPE KESEACMLVF QPDLDVDLPD LASESEVIIC LDCSSSMEG VTFLQAKQIA LHALSLVGEK QKVNIIQFGT GYKELFSYPK HITSNTMAAE FIMSATPTMG NTDFWKTLRY L SLLYPARG SRNILLVSDG HLQDESLTLQ LVKRSRPHTR LFACGIGSTA NRHVLRILSQ CGAGVFEYFN AKSKHSWRKQ IE DQMTRLC SPSCHSVSVK WQQLNPDVPE ALQAPAQVPS LFLNDRLLVY GFIPHCTQAT LCALIQEKEF RTMVSTTELQ KTT GTMIHK LAARALIRDY EDGILHENET SHEMKKQTLK SLIIKLSKEN SLITQFTSFV AVEKRDENES PFPDIPKVSE LIAK EDVDF LPYMSWQGEP QEAVRNQSLL ASSEWPELRL SKRKHRKIPF SKRKMELSQP EVSEDFEEDG LGVLPAFTSN LERGG VEKL LDLSWTESCK PTATEPLFKK VSPWETSTSS FFPILAPAVG SYLPPTARAH SPASLSFASY RQVASFGSAA PPRQFD ASQ FSQGPVPGTC ADWIPQSASC PTGPPQNPPS SPYCGIVFSG SSLSSAQSAP LQHPGGFTTR PSAGTFPELD SPQLHFS LP TDPDPIRGFG SYHPSASSPF HFQPSAASLT ANLRLPMASA LPEALCSQSR TTPVDLCLLE ESVGSLEGSR CPVFAFQS S DTESDELSEV LQDSCFLQIK CDTKDDSILC FLEVKEEDEI VCIQHWQDAV PWTELLSLQT EDGFWKLTPE LGLILNLNT NGLHSFLKQK GIQSLGVKGR ECLLDLIATM LVLQFIRTRL EKEGIVFKSL MKMDDASISR NIPWAFEAIK QASEWVRRTE GQYPSICPR LELGNDWDSA TKQLLGLQPI STVSPLHRVL HYSQG

UniProtKB: Protein mono-ADP-ribosyltransferase PARP4

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 205 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC
Details: Particles were symmetry expanded in D39 and re-extracted.
Number images used: 649317
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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