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Yorodumi- EMDB-0665: Cdc48-Ufd1/Npl4 complex processing poly-ubiquitinated substrate i... -
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-Basic information
Entry | Database: EMDB / ID: EMD-0665 | ||||||||||||
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Title | Cdc48-Ufd1/Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP | ||||||||||||
Map data | Composite map, sharpened with a B factor of -150 | ||||||||||||
Sample |
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Keywords | ATPase / ATPase complex / ubiquitin / quality control / MOTOR PROTEIN | ||||||||||||
Function / homology | Function and homology information SCF complex disassembly in response to cadmium stress / mitotic DNA replication termination / Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation / DNA replication termination ...SCF complex disassembly in response to cadmium stress / mitotic DNA replication termination / Ovarian tumor domain proteases / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / stress-induced homeostatically regulated protein degradation pathway / Hrd1p ubiquitin ligase ERAD-L complex / sister chromatid biorientation / DNA replication termination / ribophagy / RQC complex / protein localization to vacuole / mitochondria-associated ubiquitin-dependent protein catabolic process / protein-containing complex disassembly / cytoplasm protein quality control by the ubiquitin-proteasome system / positive regulation of mitochondrial fusion / HSF1 activation / nuclear protein quality control by the ubiquitin-proteasome system / endosome to plasma membrane protein transport / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein phosphatase regulator activity / Translesion Synthesis by POLH / piecemeal microautophagy of the nucleus / mating projection tip / replisome / Protein methylation / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / ribosome-associated ubiquitin-dependent protein catabolic process / nonfunctional rRNA decay / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / nuclear outer membrane-endoplasmic reticulum membrane network / KEAP1-NFE2L2 pathway / protein quality control for misfolded or incompletely synthesized proteins / Neddylation / polyubiquitin modification-dependent protein binding / autophagosome maturation / ribosomal large subunit export from nucleus / mRNA transport / ATP metabolic process / ERAD pathway / Neutrophil degranulation / rescue of stalled ribosome / ubiquitin binding / macroautophagy / positive regulation of protein localization to nucleus / modification-dependent protein catabolic process / protein tag activity / ribosome biogenesis / ribosomal large subunit assembly / ubiquitin-dependent protein catabolic process / nuclear membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / cytoplasmic translation / cytosolic large ribosomal subunit / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||||||||
Authors | Twomey EC / Ji Z | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Science / Year: 2019 Title: Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Authors: Edward C Twomey / Zhejian Ji / Thomas E Wales / Nicholas O Bodnar / Scott B Ficarro / Jarrod A Marto / John R Engen / Tom A Rapoport / Abstract: The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for ...The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear. Here, we report cryo-electron microscopy structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and polyubiquitinated substrate. The structures show that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule. The unfolded ubiquitin molecule binds to Npl4 and projects its N-terminal segment through both hexameric ATPase rings. Pore loops of the second ring form a staircase that acts as a conveyer belt to move the polypeptide through the central pore. Inducing the unfolding of ubiquitin allows the Cdc48 ATPase complex to process a broad range of substrates. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0665.map.gz | 2.2 MB | EMDB map data format | |
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Header (meta data) | emd-0665-v30.xml emd-0665.xml | 34.5 KB 34.5 KB | Display Display | EMDB header |
Images | emd_0665.png | 195.1 KB | ||
Filedesc metadata | emd-0665.cif.gz | 7 KB | ||
Others | emd_0665_additional_1.map.gz emd_0665_additional_2.map.gz emd_0665_additional_3.map.gz emd_0665_additional_4.map.gz emd_0665_additional_5.map.gz emd_0665_additional_6.map.gz emd_0665_additional_7.map.gz emd_0665_half_map_1.map.gz emd_0665_half_map_2.map.gz | 1.4 MB 28.4 MB 1.4 MB 1.5 MB 1.1 MB 1.1 MB 1.1 MB 27.9 MB 27.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0665 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0665 | HTTPS FTP |
-Validation report
Summary document | emd_0665_validation.pdf.gz | 757.8 KB | Display | EMDB validaton report |
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Full document | emd_0665_full_validation.pdf.gz | 757.4 KB | Display | |
Data in XML | emd_0665_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | emd_0665_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0665 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0665 | HTTPS FTP |
-Related structure data
Related structure data | 6oa9MC 0666C 6oaaC 6oabC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0665.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map, sharpened with a B factor of -150 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Local map for D1/Npl4 sharpened with a B factor of -100
File | emd_0665_additional_1.map | ||||||||||||
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Annotation | Local map for D1/Npl4 sharpened with a B factor of -100 | ||||||||||||
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Density Histograms |
-Additional map: Full unsharpened map from refinement
File | emd_0665_additional_2.map | ||||||||||||
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Annotation | Full unsharpened map from refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local map for D1/Npl4 sharpened with a B factor of -150
File | emd_0665_additional_3.map | ||||||||||||
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Annotation | Local map for D1/Npl4 sharpened with a B factor of -150 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local map for D1/Npl4 sharpened with a B factor of -200
File | emd_0665_additional_4.map | ||||||||||||
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Annotation | Local map for D1/Npl4 sharpened with a B factor of -200 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local map for D2 sharpened with a B factor of -100
File | emd_0665_additional_5.map | ||||||||||||
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Annotation | Local map for D2 sharpened with a B factor of -100 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local map for D2 sharpened with a B factor of -150
File | emd_0665_additional_6.map | ||||||||||||
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Annotation | Local map for D2 sharpened with a B factor of -150 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local map for D2 sharpened with a B factor of -200
File | emd_0665_additional_7.map | ||||||||||||
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Annotation | Local map for D2 sharpened with a B factor of -200 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_0665_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_0665_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the...
Entire | Name: Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP |
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Components |
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-Supramolecule #1: Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the...
Supramolecule | Name: Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Cell division control protein 48
Macromolecule | Name: Cell division control protein 48 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 92.105922 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGEEHKPLLD ASGVDPREED KTATAILRRK KKDNMLLVDD AINDDNSVIA INSNTMDKLE LFRGDTVLVK GKKRKDTVLI VLIDDELED GACRINRVVR NNLRIRLGDL VTIHPCPDIK YATRISVLPI ADTIEGITGN LFDVFLKPYF VEAYRPVRKG D HFVVRGGM ...String: MGEEHKPLLD ASGVDPREED KTATAILRRK KKDNMLLVDD AINDDNSVIA INSNTMDKLE LFRGDTVLVK GKKRKDTVLI VLIDDELED GACRINRVVR NNLRIRLGDL VTIHPCPDIK YATRISVLPI ADTIEGITGN LFDVFLKPYF VEAYRPVRKG D HFVVRGGM RQVEFKVVDV EPEEYAVVAQ DTIIHWEGEP INREDEENNM NEVGYDDIGG CRKQMAQIRE MVELPLRHPQ LF KAIGIKP PRGVLMYGPP GTGKTLMARA VANETGAFFF LINGPEVMSK MAGESESNLR KAFEEAEKNA PAIIFIDEID SIA PKRDKT NGEVERRVVS QLLTLMDGMK ARSNVVVIAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEVLRIHTK NMKL ADDVD LEALAAETHG YVGADIASLC SEAAMQQIRE KMDLIDLDED EIDAEVLDSL GVTMDNFRFA LGNSNPSALR ETVVE SVNV TWDDVGGLDE IKEELKETVE YPVLHPDQYT KFGLSPSKGV LFYGPPGTGK TLLAKAVATE VSANFISVKG PELLSM WYG ESESNIRDIF DKARAAAPTV VFLDQLDSIA KARGGSLGDA GGASDRVVNQ LLTEMDGMNA KKNVFVIGAT NRPDQID PA ILRPGRLDQL IYVPLPDENA RLSILNAQLR KTPLEPGLEL TAIAKATQGF SGADLLYIVQ RAAKYAIKDS IEAHRQHE A EKEVKVEGED VEMTDEGAKA EQEPEVDPVP YITKEHFAEA MKTAKRSVSD AELRRYEAYS QQMKASRGQF SNFNFNDAP LGTTATDNAN SNNSAPSGAG AAFGSNAEED DDLYS UniProtKB: Cell division control protein 48 |
-Macromolecule #2: Ubiquitin
Macromolecule | Name: Ubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 8.568769 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG UniProtKB: Ubiquitin-ribosomal protein eL40A fusion protein |
-Macromolecule #3: Nuclear protein localization protein 4
Macromolecule | Name: Nuclear protein localization protein 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 65.862062 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLIRFRSKNG THRVSCQEND LFGTVIEKLV GNLDPNADVD TFTVCEKPGQ GIHAVSELAD RTVMDLGLKH GDMLILNYSD KPANEKDGV NVEIGSVGID SKGIRQHRYG PLRIKELAVD EELEKEDGLI PRQKSKLCKH GDRGMCEYCS PLPPWDKEYH E KNKIKHIS ...String: MLIRFRSKNG THRVSCQEND LFGTVIEKLV GNLDPNADVD TFTVCEKPGQ GIHAVSELAD RTVMDLGLKH GDMLILNYSD KPANEKDGV NVEIGSVGID SKGIRQHRYG PLRIKELAVD EELEKEDGLI PRQKSKLCKH GDRGMCEYCS PLPPWDKEYH E KNKIKHIS FHSYLKKLNE NANKKENGSS YISPLSEPDF RINKRCHNGH EPWPRGICSK CQPSAITLQQ QEFRMVDHVE FQ KSEIINE FIQAWRYTGM QRFGYMYGSY SKYDNTPLGI KAVVEAIYEP PQHDEQDGLT MDVEQVKNEM LQIDRQAQEM GLS RIGLIF TDLSDAGAGD GSVFCKRHKD SFFLSSLEVI MAARHQTRHP NVSKYSEQGF FSSKFVTCVI SGNLEGEIDI SSYQ VSTEA EALVTADMIS GSTFPSMAYI NDTTDERYVP EIFYMKSNEY GITVKENAKP AFPVDYLLVT LTHGFPNTDT ETNSK FVSS TGFPWSNRQA MGQSQDYQEL KKYLFNVASS GDFNLLHEKI SNFHLLLYIN SLQILSPDEW KLLIESAVKN EWEESL LKL VSSAGWQTLV MILQESG UniProtKB: Nuclear protein localization protein 4 |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 9 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: GATAN CRYOPLUNGE 3 Details: Waited 20 seconds before blotting for 2.5-3 seconds.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 54.9 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127261 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2) |