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Yorodumi- EMDB-2016: CryoEM map of the p97-Ufd1-Npl4 complex in the single-binding-sit... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2016 | |||||||||
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Title | CryoEM map of the p97-Ufd1-Npl4 complex in the single-binding-site conformation | |||||||||
Map data | p97-Ufd1-Npl4 complex in the single-binding-site conformation | |||||||||
Sample |
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Keywords | p97 / Ufd1-Npl4 / asymmetric complex / ATPase | |||||||||
Biological species | Mus musculus (house mouse) / Rattus norvegicus (Norway rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Bebeacua C / Forster A / McKeown C / Meyer HH / Zhang X / Freemont PS | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Distinct conformations of the protein complex p97-Ufd1-Npl4 revealed by electron cryomicroscopy. Authors: Cecilia Bebeacua / Andreas Förster / Ciarán McKeown / Hemmo H Meyer / Xiaodong Zhang / Paul S Freemont / Abstract: p97 is a key regulator of numerous cellular pathways and associates with ubiquitin-binding adaptors to remodel ubiquitin-modified substrate proteins. How adaptor binding to p97 is coordinated and how ...p97 is a key regulator of numerous cellular pathways and associates with ubiquitin-binding adaptors to remodel ubiquitin-modified substrate proteins. How adaptor binding to p97 is coordinated and how adaptors contribute to substrate remodeling is unclear. Here we present the 3D electron cryomicroscopy reconstructions of the major Ufd1-Npl4 adaptor in complex with p97. Our reconstructions show that p97-Ufd1-Npl4 is highly dynamic and that Ufd1-Npl4 assumes distinct positions relative to the p97 ring upon addition of nucleotide. Our results suggest a model for substrate remodeling by p97 and also explains how p97-Ufd1-Npl4 could form other complexes in a hierarchical model of p97-cofactor assembly. | |||||||||
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_2016.map.gz | 668.1 KB | EMDB map data format | |
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Header (meta data) | emd-2016-v30.xml emd-2016.xml | 11 KB 11 KB | Display Display | EMDB header |
Images | emd2016fig.png | 103 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2016 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2016 | HTTPS FTP |
-Validation report
Summary document | emd_2016_validation.pdf.gz | 188.2 KB | Display | EMDB validaton report |
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Full document | emd_2016_full_validation.pdf.gz | 187.3 KB | Display | |
Data in XML | emd_2016_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2016 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2016 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2016.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | p97-Ufd1-Npl4 complex in the single-binding-site conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.53 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 : p97-Ufd1-Npl4
Entire | Name: p97-Ufd1-Npl4 |
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Components |
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-Supramolecule #1000: p97-Ufd1-Npl4
Supramolecule | Name: p97-Ufd1-Npl4 / type: sample / ID: 1000 Oligomeric state: One hexamer of p97 binds to one Ufd1-Npl4 dimer Number unique components: 3 |
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Molecular weight | Experimental: 623 KDa / Theoretical: 623 KDa |
-Macromolecule #1: p97
Macromolecule | Name: p97 / type: protein_or_peptide / ID: 1 / Name.synonym: p97 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: House mouse / Location in cell: Cytoplasm |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta |
-Macromolecule #2: Ufd1
Macromolecule | Name: Ufd1 / type: protein_or_peptide / ID: 2 / Name.synonym: Ufd1 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: House mouse / Location in cell: Cytoplasm |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta |
-Macromolecule #3: Npl4
Macromolecule | Name: Npl4 / type: protein_or_peptide / ID: 3 / Name.synonym: Npl4 / Number of copies: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) / synonym: Norway rat / Location in cell: Cytoplasm |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: Rosetta |
-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: 8 / Details: 150 mM KCL, 25 mL Tris, 2.5 mM MgCl2 |
Grid | Details: 200 mesh copper grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 2 seconds before plunging |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification |
Specialist optics | Energy filter - Name: FEI |
Date | Jul 1, 2009 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Number real images: 100 / Average electron dose: 10 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: IMAGIC / Number images used: 5000 |
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-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Protocol: Rigid Body. The protomers were fitted individually and the N-domains fitted by manual docking and refined automatically |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross Correlation |