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Yorodumi- EMDB-1505: Structural basis for the regulated protease and chaperone functio... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1505 | |||||||||
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Title | Structural basis for the regulated protease and chaperone function of DegP | |||||||||
Map data | Cryo EM structure of the DegP12-OMP complex | |||||||||
Sample |
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Keywords | protease-chaperone / electron microscopy / single particle analysis | |||||||||
Function / homology | Function and homology information intermembrane phospholipid transfer / peptidase Do / response to temperature stimulus / porin activity / protein quality control for misfolded or incompletely synthesized proteins / pore complex / chaperone-mediated protein folding / serine-type peptidase activity / cell outer membrane / protein folding ...intermembrane phospholipid transfer / peptidase Do / response to temperature stimulus / porin activity / protein quality control for misfolded or incompletely synthesized proteins / pore complex / chaperone-mediated protein folding / serine-type peptidase activity / cell outer membrane / protein folding / peptidase activity / virus receptor activity / outer membrane-bounded periplasmic space / response to heat / monoatomic ion transmembrane transport / response to oxidative stress / periplasmic space / receptor-mediated virion attachment to host cell / serine-type endopeptidase activity / DNA damage response / proteolysis / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 28.0 Å | |||||||||
Authors | Krojer T / Sawa J / Schaefer E / Saibil HR / Ehrmann M / Clausen T | |||||||||
Citation | Journal: Nature / Year: 2008 Title: Structural basis for the regulated protease and chaperone function of DegP. Authors: Tobias Krojer / Justyna Sawa / Eva Schäfer / Helen R Saibil / Michael Ehrmann / Tim Clausen / Abstract: All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in ...All organisms have to monitor the folding state of cellular proteins precisely. The heat-shock protein DegP is a protein quality control factor in the bacterial envelope that is involved in eliminating misfolded proteins and in the biogenesis of outer-membrane proteins. Here we describe the molecular mechanisms underlying the regulated protease and chaperone function of DegP from Escherichia coli. We show that binding of misfolded proteins transforms hexameric DegP into large, catalytically active 12-meric and 24-meric multimers. A structural analysis of these particles revealed that DegP represents a protein packaging device whose central compartment is adaptable to the size and concentration of substrate. Moreover, the inner cavity serves antagonistic functions. Whereas the encapsulation of folded protomers of outer-membrane proteins is protective and might allow safe transit through the periplasm, misfolded proteins are eliminated in the molecular reaction chamber. Oligomer reassembly and concomitant activation on substrate binding may also be critical in regulating other HtrA proteases implicated in protein-folding diseases. | |||||||||
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_1505.map.gz | 99.7 KB | EMDB map data format | |
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Header (meta data) | emd-1505-v30.xml emd-1505.xml | 8.7 KB 8.7 KB | Display Display | EMDB header |
Images | 1505.gif | 63.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1505 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1505 | HTTPS FTP |
-Validation report
Summary document | emd_1505_validation.pdf.gz | 288.6 KB | Display | EMDB validaton report |
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Full document | emd_1505_full_validation.pdf.gz | 288.1 KB | Display | |
Data in XML | emd_1505_validation.xml.gz | 5.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1505 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1505 | HTTPS FTP |
-Related structure data
Related structure data | 2zleMC 4a8dM 1504C 3cs0C 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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-Map
File | Download / File: emd_1505.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo EM structure of the DegP12-OMP complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.44 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 : DegP dodecamer with bound OMP
Entire | Name: DegP dodecamer with bound OMP |
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Components |
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-Supramolecule #1000: DegP dodecamer with bound OMP
Supramolecule | Name: DegP dodecamer with bound OMP / type: sample / ID: 1000 / Details: monodisperse sample / Oligomeric state: dodecameric for DegP subunits / Number unique components: 2 |
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Molecular weight | Experimental: 600 KDa |
-Macromolecule #1: DegP
Macromolecule | Name: DegP / type: protein_or_peptide / ID: 1 / Name.synonym: Heat shock protein DegP Details: proteolytically inactive DegP dodecamer with bound Omp protein Number of copies: 1 / Oligomeric state: dodecameric for DegP subunits / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.16 mg/mL |
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Staining | Type: NEGATIVE Details: embedded in vitreous ice using C-flat holey carbon grids and a Vitrobot at 20C and 100% relative humidity. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: blot for 1.5 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Sample stage | Specimen holder: liquid nitrogen-cooled cryo specimen holder Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: phase flipping |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER and IMAGIC / Details: no symmetry was use for the calculation of the map / Number images used: 6285 |