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

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Basic information

Entry
Database: PDB / ID: 2zle
TitleCryo-EM structure of DegP12/OMP
Components
  • Outer membrane protein C
  • Protease doPeptidase Do
KeywordsHYDROLASE / 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 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 28 Å
AuthorsSchaefer, E. / Saibil, H.R.
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 9, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 8, 2017Group: Other
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2

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Structure visualization

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Assembly

Deposited unit
A: Protease do
B: Protease do
C: Protease do
D: Outer membrane protein C
E: Protease do
F: Protease do
G: Protease do
H: Protease do
I: Protease do
J: Protease do
K: Protease do
L: Protease do
M: Protease do


Theoretical massNumber of molelcules
Total (without water)600,76313
Polymers600,76313
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Protease do / Peptidase Do / DegP


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 Outer membrane protein C / Porin ompC / Outer membrane protein 1B


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DegP24mer with bound Omp / Type: COMPLEX
SpecimenConc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: C-FLAT HOLEY CARBON GRIDS
VitrificationInstrument: 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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 68100 X
Image scansNum. digital images: 64

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Processing

CTF correctionDetails: phase flipping
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 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 stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms37730 0 0 0 37730

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