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Yorodumi- PDB-4a9g: Symmetrized cryo-EM reconstruction of E. coli DegQ 24-mer in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a9g | ||||||
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Title | Symmetrized cryo-EM reconstruction of E. coli DegQ 24-mer in complex with beta-casein | ||||||
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, M, N, O, P, Q, R, S, T, U, V, W, Y | ||||||
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 | 4a9g.cif.gz | 291.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a9g.ent.gz | 204.3 KB | Display | PDB format |
PDBx/mmJSON format | 4a9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a9g_validation.pdf.gz | 1003.4 KB | Display | wwPDB validaton report |
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Full document | 4a9g_full_validation.pdf.gz | 1011.9 KB | Display | |
Data in XML | 4a9g_validation.xml.gz | 102.3 KB | Display | |
Data in CIF | 4a9g_validation.cif.gz | 156.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/4a9g ftp://data.pdbj.org/pub/pdb/validation_reports/a9/4a9g | HTTPS FTP |
-Related structure data
Related structure data | 1984MC 1981C 1982C 1983C 4a8aC 4a8bC 4a8cC 4a8dC 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.: 24 / 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) / 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: DEGQ 24-MER BOUND TO BETA- CASEIN / Type: COMPLEX |
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Buffer solution | Name: 150MM NACL, 20MM HEPES/NAOH / pH: 7.5 / Details: 150MM NACL, 20MM HEPES/NAOH |
Specimen | Conc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: OTHER |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
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: -0.5 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: FULL CTF CORRECTION | ||||||||||||||||||
Symmetry | Point symmetry: O (octahedral) | ||||||||||||||||||
3D reconstruction | Method: CROSS-COMMON LINE, PROJECTION MATCHING / Resolution: 7.5 Å / Num. of particles: 9848 / Nominal pixel size: 1.4 Å / Actual pixel size: 1.4 Å Details: BETA-CASEIN WERE NOT FITTED AS BETA-CASEIN IS AN INTRISICALLY DISORDERED PROTEIN. HOWEVER BETA-CASEIN IS PRESENT IN THE DEGQ 24-MER COMPLEX. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB ...Details: BETA-CASEIN WERE NOT FITTED AS BETA-CASEIN IS AN INTRISICALLY DISORDERED PROTEIN. HOWEVER BETA-CASEIN IS PRESENT IN THE DEGQ 24-MER COMPLEX. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1984. (DEPOSITION ID: 10375). Symmetry type: POINT | ||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--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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