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- EMDB-44960: Human Vault Cage in complex with the MINT domain of PARP4 -

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Basic information

Entry
Database: EMDB / ID: EMD-44960
TitleHuman Vault Cage in complex with the MINT domain of PARP4
Map dataSharpened cryo-EM map of the human MVP-MINT domain complex
Sample
  • Complex: Binary complex of the PARP4 MINT domain bound to oligomerized human MVP
    • Protein or peptide: Major Vault Protein
    • Protein or peptide: Poly(ADP-Ribose) Polymerase 4
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 / : / Maturation of nucleoprotein / ERBB signaling pathway / Maturation of nucleoprotein / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity ...negative regulation of protein tyrosine kinase activity / protein activation cascade / negative regulation of protein autophosphorylation / : / Maturation of nucleoprotein / ERBB signaling pathway / Maturation of nucleoprotein / NAD+-protein-aspartate ADP-ribosyltransferase activity / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / negative regulation of epidermal growth factor receptor signaling pathway / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / mRNA transport / nuclear pore / nucleotidyltransferase activity / spindle microtubule / protein modification process / protein transport / secretory granule lumen / protein phosphatase binding / ficolin-1-rich granule lumen / cytoskeleton / cell population proliferation / response to xenobiotic stimulus / inflammatory response / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / BRCT domain profile. / von Willebrand factor, type A / 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: 3.4 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: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
History
DepositionMay 20, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44960.png

Downloads & links

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Map

FileDownload / File: emd_44960.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-MINT domain complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 800 pix.
= 1080. Å		1.35 Å/pix.
x 800 pix.
= 1080. Å		1.35 Å/pix.
x 800 pix.
= 1080. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.6594215 - 1.3203635
Average (Standard dev.)-0.0006483623 (±0.04163186)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 1080.0 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-MINT domain complex

Fileemd_44960_additional_1.map
AnnotationUnsharpened cryo-EM map of the human MVP-MINT domain 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-MINT domain complex

Fileemd_44960_half_map_1.map
AnnotationCryo-EM half map of the human MVP-MINT domain 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-MINT domain complex

Fileemd_44960_half_map_2.map
AnnotationCryo-EM half map of the human MVP-MINT domain 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 the PARP4 MINT domain bound to oligomerized hum...

EntireName: Binary complex of the PARP4 MINT domain bound to oligomerized human MVP
Components
  • Complex: Binary complex of the PARP4 MINT domain bound to oligomerized human MVP
    • Protein or peptide: Major Vault Protein
    • Protein or peptide: Poly(ADP-Ribose) Polymerase 4

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Supramolecule #1: Binary complex of the PARP4 MINT domain bound to oligomerized hum...

SupramoleculeName: Binary complex of the PARP4 MINT domain bound to oligomerized human MVP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.5 MDa

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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: 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: Poly(ADP-Ribose) Polymerase 4

MacromoleculeName: Poly(ADP-Ribose) Polymerase 4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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: 7.4
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
1.5 mMMgCl2Magnesium chloride
150.0 mMNaClSodium chloride
1.0 mMC4H10O2S2DTT

Details: 50 mM Tris,pH 7.4 1.5 mM MgCl2, 150 mM NaCl, 1 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 opticsEnergy filter - Name: GIF Bioquantum
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2728 / Average electron dose: 50.0 e/Å2
Details: Images were collected in movie mode, with 40 frames per image.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
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: 96257
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1)
Details: CTF correction was performed when movies were imported into cryoSPARC Live
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1)
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: 19104
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 50 / Avg.num./class: 441 / Software - Name: cryoSPARC (ver. 3.3.1)
FSC plot (resolution estimation)

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