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- EMDB-44955: Human Vault Cage in complex with PARP4 -

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Basic information

Entry
Database: EMDB / ID: EMD-44955
TitleHuman Vault Cage in complex with PARP4
Map dataSharpened cryo-EM map of the human MVP-PARP4 complex
Sample
  • Complex: Binary complex of human PARP4 bound to oligomerized human MVP
    • Protein or peptide: Major vault protein
    • Protein or peptide: Protein mono-ADP-ribosyltransferase PARP4
KeywordsVault / Vault Cage / MVP / Major Vault Protein / SPFH / PARP4 / Poly(ADP-ribose)Polymerase 4 / MINT / Poly(ADP-ribose)Polymerase / Ribonucleoprotein / Megadalton complex / TEP1 / vault RNA / PROTEIN TRANSPORT
Function / homology
Function and homology information


negative regulation of protein tyrosine kinase activity / protein activation cascade / negative regulation of protein autophosphorylation / Nicotinamide salvage / Maturation of nucleoprotein / Maturation of nucleoprotein / ERBB signaling pathway / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity ...negative regulation of protein tyrosine kinase activity / protein activation cascade / negative regulation of protein autophosphorylation / Nicotinamide salvage / Maturation of nucleoprotein / Maturation of nucleoprotein / ERBB signaling pathway / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE2 glutamate ADP-ribosyltransferase activity / NAD+-histone H2BE18 glutamate ADP-ribosyltransferase activity / negative regulation of epidermal growth factor receptor signaling pathway / NAD+-protein mono-ADP-ribosyltransferase activity / NAD+ poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / mRNA transport / nuclear pore / nucleotidyltransferase activity / spindle microtubule / protein modification process / protein transport / protein phosphatase binding / secretory granule lumen / ficolin-1-rich granule lumen / cell population proliferation / cytoskeleton / inflammatory response / response to xenobiotic stimulus / ribonucleoprotein complex / DNA repair / DNA damage response / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Protein mono-ADP-ribosyltransferase PARP4 / 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 ...Protein mono-ADP-ribosyltransferase PARP4 / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / BRCT domain profile. / BRCT domain / BRCT domain superfamily / 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: 2.9 Å
AuthorsLodwick JE / Zhao M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM143052 United States
CitationJournal: Science / Year: 2009
Title: The structure of rat liver vault at 3.5 angstrom resolution.
Authors: Hideaki Tanaka / Koji Kato / Eiki Yamashita / Tomoyuki Sumizawa / Yong Zhou / Min Yao / Kenji Iwasaki / Masato Yoshimura / Tomitake Tsukihara /
Abstract: Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the ...Vaults are among the largest cytoplasmic ribonucleoprotein particles and are found in numerous eukaryotic species. Roles in multidrug resistance and innate immunity have been suggested, but the cellular function remains unclear. We have determined the x-ray structure of rat liver vault at 3.5 angstrom resolution and show that the cage structure consists of a dimer of half-vaults, with each half-vault comprising 39 identical major vault protein (MVP) chains. Each MVP monomer folds into 12 domains: nine structural repeat domains, a shoulder domain, a cap-helix domain, and a cap-ring domain. Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells.
History
DepositionMay 20, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44955.png

Downloads & links

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Map

FileDownload / File: emd_44955.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM map of the human MVP-PARP4 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 800 pix.
= 1056. Å		1.32 Å/pix.
x 800 pix.
= 1056. Å		1.32 Å/pix.
x 800 pix.
= 1056. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-1.118702 - 2.0248065
Average (Standard dev.)-0.0013360112 (±0.05846054)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1056.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened cryo-EM map of the human MVP-PARP4 complex

Fileemd_44955_additional_1.map
AnnotationUnsharpened cryo-EM map of the human MVP-PARP4 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map of the human MVP-PARP4 complex

Fileemd_44955_half_map_1.map
AnnotationCryo-EM half map of the human MVP-PARP4 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map of the human MVP-PARP4 complex

Fileemd_44955_half_map_2.map
AnnotationCryo-EM half map of the human MVP-PARP4 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of human PARP4 bound to oligomerized human MVP

EntireName: Binary complex of human PARP4 bound to oligomerized human MVP
Components
  • Complex: Binary complex of human PARP4 bound to oligomerized human MVP
    • Protein or peptide: Major vault protein
    • Protein or peptide: Protein mono-ADP-ribosyltransferase PARP4

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Supramolecule #1: Binary complex of human PARP4 bound to oligomerized human MVP

SupramoleculeName: Binary complex of human PARP4 bound to oligomerized human MVP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.7 MDa

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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: Trichoplusia ni (cabbage looper)
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: 2 / Enantiomer: LEVO
EC number: Transferases; Glycosyltransferases; Pentosyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 192.810172 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
5.0 mMMgCl2Magnesium chloride
5.0 mMCaCl2Calcium chloride
0.25 mMC4H10O2S2DTT

Details: 50 mM HEPES, 5 mM MgCl2, 5 mM CaCl2, 0.25 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 14 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER
Details: Quantifoil grids with a 2 nm continuous carbon coating were subjected to a 15 s, 5W plasma cleaning program in O2 gas
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: Vitrification carried out under standard conditions.
DetailsSample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector with two hexapole elements
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 8 eV
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 7491 / Average electron dose: 45.0 e/Å2
Details: Images were collected in movie mode, with 40 frames per image. Data was collected in SerialEM using a strategy of 3 by 3 + 1 shots per hole.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 670079
Startup modelType of model: OTHER / Details: EM map from a previous dataset we collected
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D39 (2x39 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4)
Software - details: cryoSPARC Homogeneous Refinement was performed. The program was instructed to optimize the per-particle defocus and per-exposure-group CTF parameters, fit the anisotropic beam ...Software - details: cryoSPARC Homogeneous Refinement was performed. The program was instructed to optimize the per-particle defocus and per-exposure-group CTF parameters, fit the anisotropic beam magnification, and apply Ewald sphere correction using the correct curvature sign.
Number images used: 44443
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final 3D classificationNumber classes: 50 / Avg.num./class: 2640 / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4v60


Chain - Chain ID: A / Chain - Residue range: 1-845 / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsThe starting model was the rat homologue of MVP from a previous crystal structure of the vault cage (PDB accession no 4V60). The final model was refined in real space and validated using PHENIX.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9bw6:
Human Vault Cage in complex with PARP4

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Atomic model buiding 2

Initial modelPDB ID:

ukk3


Chain - Chain ID: A / Chain - Residue range: 1562-1724 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsPARP4's MINT domain, predicted by AlphaFold2, was used as the starting model. The final model was refined in real space and validated using PHENIX.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9bw6:
Human Vault Cage in complex with PARP4

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