+Open data
-Basic information
Entry | Database: PDB / ID: 2zle | ||||||
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Title | Cryo-EM structure of DegP12/OMP | ||||||
Components |
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Keywords | HYDROLASE / DegP / HtrA / protease / chaperone / PDZ / outer membrane protein / OMP / periplasm / Serine protease / Stress response / Ion transport / Phage recognition / Porin / Transmembrane / Transport | ||||||
Function / homology | Function and homology information peptidase Do / response to temperature stimulus / porin activity / protein quality control for misfolded or incompletely synthesized proteins / pore complex / chaperone-mediated protein folding / monoatomic ion transmembrane transport / serine-type peptidase activity / cell outer membrane / virus receptor activity ...peptidase Do / response to temperature stimulus / porin activity / protein quality control for misfolded or incompletely synthesized proteins / pore complex / chaperone-mediated protein folding / monoatomic ion transmembrane transport / serine-type peptidase activity / cell outer membrane / virus receptor activity / protein folding / peptidase activity / outer membrane-bounded periplasmic space / response to heat / response to oxidative stress / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 28 Å | ||||||
Authors | Schaefer, E. / Saibil, H.R. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2zle.cif.gz | 969.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zle.ent.gz | 756.8 KB | Display | PDB format |
PDBx/mmJSON format | 2zle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zle_validation.pdf.gz | 891.3 KB | Display | wwPDB validaton report |
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Full document | 2zle_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2zle_validation.xml.gz | 222.8 KB | Display | |
Data in CIF | 2zle_validation.cif.gz | 311.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/2zle ftp://data.pdbj.org/pub/pdb/validation_reports/zl/2zle | HTTPS FTP |
-Related structure data
Related structure data | 1505MC 1504C 3cs0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 46868.926 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: degP, htrA, ptd / Production host: Escherichia coli (E. coli) References: UniProt: P0C0V0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Protein | | Mass: 38336.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompC, meoA, par / Production host: Escherichia coli (E. coli) / References: UniProt: P06996 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DegP24mer with bound Omp / Type: COMPLEX |
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Specimen | Conc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: C-FLAT HOLEY CARBON GRIDS |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: Embedded in vitreous ice using C-flat holey carbon grids (CF-2/2-4C-100, Protochip) and a Vitrobot (FEI) at 20 temperature and 100% relative humidity |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 68100 X |
Image scans | Num. digital images: 64 |
-Processing
CTF correction | Details: phase flipping | ||||||||||||
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 28 Å / Num. of particles: 6285 / Nominal pixel size: 4.44 Å Details: This structure is docking of four DegP trimers (PDB ID 1KY9) and an OmpC monomer (PDB ID 2J1N) into an EM map by hand at 28A resolution. At this low resolution, no exact fitting can be done. Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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