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Yorodumi- EMDB-20730: Cryo-EM structure of p97-A232E mutant bound to cofactors UFD1L an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20730 | |||||||||
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Title | Cryo-EM structure of p97-A232E mutant bound to cofactors UFD1L and NPLOC4 | |||||||||
Map data | Cryo-EM structure of the p97-A232E:NPLOC4-UFD1L complex | |||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.26 Å | |||||||||
Authors | Blythe EE / Gates SN / Deshaies RJ / Martin A | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Structure / Year: 2019 Title: Multisystem Proteinopathy Mutations in VCP/p97 Increase NPLOC4·UFD1L Binding and Substrate Processing. Authors: Emily E Blythe / Stephanie N Gates / Raymond J Deshaies / Andreas Martin / Abstract: Valosin-containing protein (VCP)/p97 is an essential ATP-dependent protein unfoldase. Dominant mutations in p97 cause multisystem proteinopathy (MSP), a disease affecting the brain, muscle, and bone. ...Valosin-containing protein (VCP)/p97 is an essential ATP-dependent protein unfoldase. Dominant mutations in p97 cause multisystem proteinopathy (MSP), a disease affecting the brain, muscle, and bone. Despite the identification of numerous pathways that are perturbed in MSP, the molecular-level defects of these p97 mutants are not completely understood. Here, we use biochemistry and cryoelectron microscopy to explore the effects of MSP mutations on the unfoldase activity of p97 in complex with its substrate adaptor NPLOC4⋅UFD1L (UN). We show that all seven analyzed MSP mutants unfold substrates faster. Mutant homo- and heterohexamers exhibit tighter UN binding and faster substrate processing. Our structural studies suggest that the increased UN affinity originates from a decoupling of p97's nucleotide state and the positioning of its N-terminal domains. Together, our data support a gain-of-function model for p97-UN-dependent processes in MSP and underscore the importance of N-terminal domain movements for adaptor recruitment and substrate processing by p97. | |||||||||
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_20730.map.gz | 7.7 MB | EMDB map data format | |
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Header (meta data) | emd-20730-v30.xml emd-20730.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_20730_fsc.xml | 9.2 KB | Display | FSC data file |
Images | emd_20730.png | 211.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20730 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20730 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20730.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of the p97-A232E:NPLOC4-UFD1L complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 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 : Complex of p97-A232E and cofactors UFD1L and NPLOC4
Entire | Name: Complex of p97-A232E and cofactors UFD1L and NPLOC4 |
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Components |
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-Supramolecule #1: Complex of p97-A232E and cofactors UFD1L and NPLOC4
Supramolecule | Name: Complex of p97-A232E and cofactors UFD1L and NPLOC4 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET24b |
Molecular weight | Theoretical: 191 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 20.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Gatan Solarus Plasma Cleaner | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV / Details: 2 second blot, 3 second wait. | |||||||||||||||||||||
Details | Incubate complex for 5 minutes at 37 degrees Celsius before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Number real images: 5897 / Average exposure time: 8.0 sec. / Average electron dose: 48.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |