+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20149 | |||||||||
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Title | Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) | |||||||||
Map data | Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) | |||||||||
Sample |
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Keywords | Cdc48 / AAA+ ATPase / substrate translocation / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information SCF complex disassembly in response to cadmium stress / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / ribophagy / DNA replication termination / Neddylation / stress-induced homeostatically regulated protein degradation pathway ...SCF complex disassembly in response to cadmium stress / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / endoplasmic reticulum membrane fusion / Cdc48p-Npl4p-Vms1p AAA ATPase complex / Doa10p ubiquitin ligase complex / ribophagy / DNA replication termination / Neddylation / stress-induced homeostatically regulated protein degradation pathway / positive regulation of mitochondrial fusion / sister chromatid biorientation / ascospore formation / cytoplasm protein quality control by the ubiquitin-proteasome system / Hrd1p ubiquitin ligase ERAD-L complex / RQC complex / protein-containing complex disassembly / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / HSF1 activation / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / nonfunctional rRNA decay / nuclear membrane reassembly / protein phosphatase regulator activity / piecemeal microautophagy of the nucleus / mating projection tip / mitotic spindle disassembly / replisome / VCP-NPL4-UFD1 AAA ATPase complex / vesicle-fusing ATPase / : / ribosome-associated ubiquitin-dependent protein catabolic process / retrograde protein transport, ER to cytosol / protein quality control for misfolded or incompletely synthesized proteins / glycogen metabolic process / Golgi organization / autophagosome maturation / autophagosome assembly / polyubiquitin modification-dependent protein binding / rescue of stalled ribosome / : / ATP metabolic process / Neutrophil degranulation / ubiquitin binding / macroautophagy / positive regulation of protein localization to nucleus / proteasome-mediated ubiquitin-dependent protein catabolic process / membrane fusion / endoplasmic reticulum membrane / 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: 3.7 Å | |||||||||
Authors | Cooney I / Han H / Stewart M / Carson RH / Hansen D / Price JC / Hill CP / Shen PS | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Science / Year: 2019 Title: Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Authors: Ian Cooney / Han Han / Michael G Stewart / Richard H Carson / Daniel T Hansen / Janet H Iwasa / John C Price / Christopher P Hill / Peter S Shen / Abstract: The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite ...The cellular machine Cdc48 functions in multiple biological pathways by segregating its protein substrates from a variety of stable environments such as organelles or multi-subunit complexes. Despite extensive studies, the mechanism of Cdc48 has remained obscure, and its reported structures are inconsistent with models of substrate translocation proposed for other AAA+ ATPases (adenosine triphosphatases). Here, we report a 3.7-angstrom-resolution structure of Cdc48 in complex with an adaptor protein and a native substrate. Cdc48 engages substrate by adopting a helical configuration of substrate-binding residues that extends through the central pore of both of the ATPase rings. These findings indicate a unified hand-over-hand mechanism of protein translocation by Cdc48 and other AAA+ ATPases. | |||||||||
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_20149.map.gz | 49.5 MB | EMDB map data format | |
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Header (meta data) | emd-20149-v30.xml emd-20149.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd_20149.png | 130.2 KB | ||
Filedesc metadata | emd-20149.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20149 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20149 | HTTPS FTP |
-Related structure data
Related structure data | 6opcMC 6ombC M: atomic model generated by this map C: citing same article (ref.) |
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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_20149.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cdc48 Hexamer in a complex with substrate and Shp1(Ubx Domain) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.168 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Cdc48-Substrate Complex
Entire | Name: Cdc48-Substrate Complex |
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Components |
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-Supramolecule #1: Cdc48-Substrate Complex
Supramolecule | Name: Cdc48-Substrate Complex / 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: 92.106914 KDa |
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 VFLDELDSIA 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: Substrate bound to the central pore of the Cdc48 hexamer
Macromolecule | Name: Substrate bound to the central pore of the Cdc48 hexamer type: protein_or_peptide / ID: 2 / Details: co-purified with Cdc48 hexamer / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 1.890321 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-Macromolecule #3: UBX domain-containing protein 1
Macromolecule | Name: UBX domain-containing protein 1 / 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: 47.041105 KDa |
Sequence | String: MAEIPDETIQ QFMALTNVSH NIAVQYLSEF GDLNEALNSY YASQTDDQKD RREEAHWNRQ QEKALKQEAF STNSSNKAIN TEHVGGLCP KPGSSQGSNE YLKRKGSTSP EPTKGSSRSG SGNNSRFMSF SDMVRGQADD DDEDQPRNTF AGGETSGLEV T DPSDPNSL ...String: MAEIPDETIQ QFMALTNVSH NIAVQYLSEF GDLNEALNSY YASQTDDQKD RREEAHWNRQ QEKALKQEAF STNSSNKAIN TEHVGGLCP KPGSSQGSNE YLKRKGSTSP EPTKGSSRSG SGNNSRFMSF SDMVRGQADD DDEDQPRNTF AGGETSGLEV T DPSDPNSL LKDLLEKARR GGQMGAENGF RDDEDHEMGA NRFTGRGFRL GSTIDAADEV VEDNTSQSQR RPEKVTREIT FW KEGFQVA DGPLYRYDDP ANSFYLSELN QGRAPLKLLD VQFGQEVEVN VYKKLDESYK APTRKLGGFS GQGQRLGSPI PGE SSPAEV PKNETPAAQE QPMPDNEPKQ GDTSIQIRYA NGKREVLHCN STDTVKFLYE HVTSNANTDP SRNFTLNYAF PIKP ISNDE TTLKDADLLN SVVVQRWA UniProtKB: UBX domain-containing protein 1 |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 10 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #5: BERYLLIUM TRIFLUORIDE ION
Macromolecule | Name: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 5 / Number of copies: 8 / Formula: BEF |
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Molecular weight | Theoretical: 66.007 Da |
Chemical component information | ChemComp-BEF: |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: ab initio |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54367 |