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Yorodumi- PDB-4a8c: Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a8c | ||||||
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Title | Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with a binding peptide | ||||||
Components | PERIPLASMIC PH-DEPENDENT SERINE ENDOPROTEASE DEGQ | ||||||
Keywords | HYDROLASE / CHAPERONE | ||||||
Function / homology | Function and homology information peptidase Do / protein quality control for misfolded or incompletely synthesized proteins / proteolysis involved in protein catabolic process / peptidase activity / periplasmic space / serine-type endopeptidase activity / identical protein binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.5 Å | ||||||
Model type details | CA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K, L | ||||||
Authors | Malet, H. / Canellas, F. / Sawa, J. / Yan, J. / Thalassinos, K. / Ehrmann, M. / Clausen, T. / Saibil, H.R. | ||||||
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. | ||||||
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 | 4a8c.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a8c.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 4a8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a8c_validation.pdf.gz | 850.2 KB | Display | wwPDB validaton report |
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Full document | 4a8c_full_validation.pdf.gz | 856.5 KB | Display | |
Data in XML | 4a8c_validation.xml.gz | 57.2 KB | Display | |
Data in CIF | 4a8c_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/4a8c ftp://data.pdbj.org/pub/pdb/validation_reports/a8/4a8c | HTTPS FTP |
-Related structure data
Related structure data | 1983MC 1981C 1982C 1984C 4a8aC 4a8bC 4a8dC 4a9gC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 45542.664 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39099, peptidase Do Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 214 TO ALA ENGINEERED RESIDUE IN CHAIN B, SER 214 TO ALA ...ENGINEERED | |
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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: ESCHERICHIA COLI DEGQ 12- MER IN COMPLEX WITH A BINDING PEPTIDE Type: COMPLEX |
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Buffer solution | Name: 20 MM HEPES/NAOH, 150 MM NACL / pH: 7.5 / Details: 20 MM HEPES/NAOH, 150 MM NACL |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- MANUAL PLUNGER, METHOD- BLOT FOR 2 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Details: LOW DOSE MODE |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 50000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm |
Specimen holder | Temperature: 91 K / Tilt angle max: 0 ° / Tilt angle min: -0.1 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 110 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: PHASE FLIPPING, FULL CTF CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: D3 (2x3 fold dihedral) | ||||||||||||||||||||||||
3D reconstruction | Method: COMMON LINE, PROJECTION MATCHING / Resolution: 7.5 Å / Num. of particles: 29432 / Nominal pixel size: 1.4 Å / Actual pixel size: 1.4 Å Details: DEGQ 12-MER WERE OBTAINED IN PRESENCE OF A PEPTIDE. THE PEPTIDE SEQUENCE IS SPMFKGVLDMMYGGMRGYQV THE NUMBER OF PEPTIDES BOUND TO DEGQ 12-MER IS UNKNOWN. THE PEPTIDES ARE NOT MODELLED DUE TO ...Details: DEGQ 12-MER WERE OBTAINED IN PRESENCE OF A PEPTIDE. THE PEPTIDE SEQUENCE IS SPMFKGVLDMMYGGMRGYQV THE NUMBER OF PEPTIDES BOUND TO DEGQ 12-MER IS UNKNOWN. THE PEPTIDES ARE NOT MODELLED DUE TO THE RESOLUTION OF THE MAP. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1983. (DEPOSITION ID: 10374). Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--RIGID BODY AND FLEXIBLE FITTING REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 3STJ Accession code: 3STJ / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
Refinement | Highest resolution: 7.5 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.5 Å
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