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- EMDB-1504: Structural basis for the regulated protease and chaperone functio... -

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Basic information

Entry
Database: EMDB / ID: EMD-1504
TitleStructural basis for the regulated protease and chaperone function of DegP
Map datanegative stain EM structure of the DegP24-OMP complex
Sample
  • Sample: proteolytically inactive DegP24mer with bound Omp protein
  • Protein or peptide: protease
Keywordsprotease-chaperone / electron microscopy / single particle analysis
Function / homology
Function and homology information


peptidase Do / programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / response to heat / outer membrane-bounded periplasmic space ...peptidase Do / programmed cell death / response to temperature stimulus / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein folding / serine-type peptidase activity / protein folding / peptidase activity / response to heat / outer membrane-bounded periplasmic space / response to oxidative stress / periplasmic space / positive regulation of apoptotic process / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Peptidase S1C, Do / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Periplasmic serine endoprotease DegP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / negative staining / Resolution: 23.0 Å
AuthorsKrojer T / Sawa J / Schaefer E / Saibil HR / Ehrmann M / Clausen T
CitationJournal: 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
DepositionApr 7, 2008-
Header (metadata) releaseApr 8, 2008-
Map releaseMar 31, 2009-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3cs0
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1504.gif

Downloads & links

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Map

FileDownload / File: emd_1504.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnegative stain EM structure of the DegP24-OMP complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.44 Å/pix.
x 130 pix.
= 577.2 Å		4.44 Å/pix.
x 130 pix.
= 577.2 Å		4.44 Å/pix.
x 130 pix.
= 577.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.44 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0127 / Movie #1: 0.009
Minimum - Maximum-0.0834089 - 0.115691
Average (Standard dev.)-0.000151646 (±0.00515611)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 577.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.444.444.44
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z577.200577.200577.200
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-0.0830.116-0.000

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Supplemental data

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Sample components

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Entire : proteolytically inactive DegP24mer with bound Omp protein

EntireName: proteolytically inactive DegP24mer with bound Omp protein
Components
  • Sample: proteolytically inactive DegP24mer with bound Omp protein
  • Protein or peptide: protease

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Supramolecule #1000: proteolytically inactive DegP24mer with bound Omp protein

SupramoleculeName: proteolytically inactive DegP24mer with bound Omp protein
type: sample / ID: 1000 / Details: monodisperse sample / Oligomeric state: 24mer / Number unique components: 2
Molecular weightExperimental: 1.13 MDa

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Macromolecule #1: protease

MacromoleculeName: protease / type: protein_or_peptide / ID: 1 / Name.synonym: DegP
Details: proteolytically inactive DegP24mer with bound Omp protein
Number of copies: 1 / Oligomeric state: 24 / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.0064 mg/mL
StainingType: NEGATIVE
Details: negatively stained with 2% (w/v) uranyl acetate on glow discharged, carbon-coated grids
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Sample stageSpecimen holder: single tilt / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF
Details: octahedral symmetry was used for the reconstruction

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