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- PDB-4a8d: DegP dodecamer with bound OMP -

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Basic information

Entry
Database: PDB / ID: 4a8d
TitleDegP dodecamer with bound OMP
Components
  • OUTER MEMBRANE PROTEIN C
  • PERIPLASMIC SERINE ENDOPROTEASE DEGP
KeywordsHYDROLASE/TRANSPORT PROTEIN / HYDROLASE-TRANSPORT PROTEIN COMPLEX / CHAPERONE
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
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 ...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
Model type detailsCA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L, M
AuthorsMalet, H. / Krojer, T. / Sawa, J. / Schafer, E. / Saibil, H.R. / Ehrmann, M. / Clausen, T.
Citation
Journal: Nat Struct Mol Biol / Year: 2012
Title: Newly folded substrates inside the molecular cage of the HtrA chaperone DegQ.
Authors: Hélène Malet / Flavia Canellas / Justyna Sawa / Jun Yan / Konstantinos Thalassinos / Michael Ehrmann / Tim Clausen / Helen R Saibil /
Abstract: The HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA ...The HtrA protein family combines chaperone and protease activities and is essential for protein quality control in many organisms. Whereas the mechanisms underlying the proteolytic function of HtrA proteins are well characterized, their chaperone activity remains poorly understood. Here we describe cryo-EM structures of Escherichia coli DegQ in its 12- and 24-mer states in complex with model substrates, providing a structural model of HtrA chaperone action. Up to six lysozyme substrates bind inside the DegQ 12-mer cage and are visualized in a close-to-native state. An asymmetric reconstruction reveals the binding of a well-ordered lysozyme to four DegQ protomers. DegQ PDZ domains are located adjacent to substrate density and their presence is required for chaperone activity. The substrate-interacting regions appear conserved in 12- and 24-mer cages, suggesting a common mechanism of chaperone function.
#1: 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
DepositionNov 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Movie
  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
A: PERIPLASMIC SERINE ENDOPROTEASE DEGP
B: PERIPLASMIC SERINE ENDOPROTEASE DEGP
C: PERIPLASMIC SERINE ENDOPROTEASE DEGP
D: PERIPLASMIC SERINE ENDOPROTEASE DEGP
E: PERIPLASMIC SERINE ENDOPROTEASE DEGP
F: PERIPLASMIC SERINE ENDOPROTEASE DEGP
G: PERIPLASMIC SERINE ENDOPROTEASE DEGP
H: PERIPLASMIC SERINE ENDOPROTEASE DEGP
I: PERIPLASMIC SERINE ENDOPROTEASE DEGP
J: PERIPLASMIC SERINE ENDOPROTEASE DEGP
K: PERIPLASMIC SERINE ENDOPROTEASE DEGP
L: PERIPLASMIC SERINE ENDOPROTEASE DEGP
M: OUTER MEMBRANE PROTEIN C


Theoretical massNumber of molelcules
Total (without water)600,57113
Polymers600,57113
Non-polymers00
Water00
1


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

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Components

#1: Protein
PERIPLASMIC SERINE ENDOPROTEASE DEGP / HEAT SHOCK PROTEIN DEGP / PROTEASE DO / DEGP / Coordinate model: Cα atoms only


Mass: 46852.926 Da / Num. of mol.: 12 / Fragment: DEGP / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CLC198 / References: UniProt: P0C0V0, peptidase Do
#2: Protein OUTER MEMBRANE PROTEIN C / OUTER MEMBRANE PROTEIN 1B / PORIN OMPC / OMP / Coordinate model: Cα atoms only


Mass: 38336.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: CLC198 / References: UniProt: P06996
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 236 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN C, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN D, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN E, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN F, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN G, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN H, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN I, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN J, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN K, SER 236 TO ALA ENGINEERED RESIDUE IN CHAIN L, SER 236 TO ALA

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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: DEGP DODECAMER BOUND TO OMP / Type: COMPLEX
Buffer solutionName: 300MM NACL, 50MM HEPES- NAOH / pH: 8 / Details: 300MM NACL, 50MM HEPES- NAOH
SpecimenConc.: 0.16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: OTHER
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: EMBEDDED IN VITREOUS ICE USING C-FLAT HOLEY CARBON GRIDS AND A VITROBOT AT 20C.

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 68100 X / Calibrated magnification: 68100 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2 mm
Specimen holderTemperature: 91 K / Tilt angle max: 0 ° / Tilt angle min: -0.5 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: GENERIC CCD
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1IMAGIC3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: PHASE FLIPPING
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 28 Å / Num. of particles: 6285 / Nominal pixel size: 4.44 Å / Actual pixel size: 4.44 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1505(DEPOSITION ID: 6111).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RIGID BODY FITTING REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3CS0

3cs0


Accession code: 3CS0 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 28 Å
Refinement stepCycle: LAST / Highest resolution: 28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4954 0 0 0 4954

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