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- EMDB-1505: Structural basis for the regulated protease and chaperone functio... -

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Basic information

Entry
Database: EMDB / ID: EMD-1505
TitleStructural basis for the regulated protease and chaperone function of DegP
Map dataCryo EM structure of the DegP12-OMP complex
Sample
  • Sample: DegP dodecamer with bound OMP
  • Protein or peptide: DegPPeptidase Do
Keywordsprotease-chaperone / electron microscopy / single particle analysis
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 / protein folding ...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 / protein folding / virus receptor activity / outer membrane-bounded periplasmic space / peptidase activity / response to heat / response to oxidative stress / receptor-mediated virion attachment to host cell / periplasmic space / serine-type endopeptidase activity / DNA damage response / proteolysis / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Peptidase S1C, Do / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / Peptidase S1C / Trypsin-like peptidase domain / Porin domain superfamily / PDZ domain ...Peptidase S1C, Do / Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / Peptidase S1C / Trypsin-like peptidase domain / Porin domain superfamily / 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
Outer membrane porin C / Periplasmic serine endoprotease DegP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 28.0 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: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2zle
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4a8d
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1505.gif

Downloads & links

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Map

FileDownload / File: emd_1505.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo EM structure of the DegP12-OMP complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.44 Å/pix.
x 100 pix.
= 444. Å		4.44 Å/pix.
x 100 pix.
= 444. Å		4.44 Å/pix.
x 100 pix.
= 444. 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 LevelBy AUTHOR: 0.0127 / Movie #1: 0.2
Minimum - Maximum-0.694379 - 1.05933
Average (Standard dev.)0.0000112379 (±0.04999956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-50-50-50
Dimensions100100100
Spacing100100100
CellA=B=C: 444 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.444.444.44
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z444.000444.000444.000
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S123
start NC/NR/NS-50-50-50
NC/NR/NS100100100
D min/max/mean-0.6941.0590.000

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Supplemental data

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Sample components

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Entire : DegP dodecamer with bound OMP

EntireName: DegP dodecamer with bound OMP
Components
  • Sample: DegP dodecamer with bound OMP
  • Protein or peptide: DegPPeptidase Do

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Supramolecule #1000: DegP dodecamer with bound OMP

SupramoleculeName: DegP dodecamer with bound OMP / type: sample / ID: 1000 / Details: monodisperse sample / Oligomeric state: dodecameric for DegP subunits / Number unique components: 2
Molecular weightExperimental: 600 KDa

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Macromolecule #1: DegP

MacromoleculeName: 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
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.16 mg/mL
StainingType: NEGATIVE
Details: embedded in vitreous ice using C-flat holey carbon grids and a Vitrobot at 20C and 100% relative humidity.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: vitrobot / Method: blot for 1.5 seconds before plunging

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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: liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: phase flipping
Final reconstructionApplied 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

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Atomic model buiding 1

Initial model(PDB ID:

1ky9

,

2j1n

)
DetailsDegP trimers and OmpC monomer were use for manual docking in Chimera. The fit will be deposited in the PDB data bank.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2zle:
Cryo-EM structure of DegP12/OMP

PDB-4a8d:
DegP dodecamer with bound OMP

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