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- EMDB-1981: Asymmetric cryo-EM reconstruction of E. coli DegQ 12-mer in compl... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1981 | |||||||||
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Title | Asymmetric cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozyme | |||||||||
![]() | Asymmetric cryo-EM map of E. coli DegQ 12-mer in complex with lysozyme | |||||||||
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![]() | Chaperone / Protease | |||||||||
Function / homology | ![]() peptidase Do / programmed cell death / protein quality control for misfolded or incompletely synthesized proteins / Lactose synthesis / Antimicrobial peptides / proteolysis involved in protein catabolic process / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme ...peptidase Do / programmed cell death / protein quality control for misfolded or incompletely synthesized proteins / Lactose synthesis / Antimicrobial peptides / proteolysis involved in protein catabolic process / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / peptidase activity / defense response to Gram-negative bacterium / killing of cells of another organism / periplasmic space / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of apoptotic process / serine-type endopeptidase activity / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.2 Å | |||||||||
![]() | Malet H / Canellas F / Sawa J / Yan J / Thalassinos K / Ehrmann M / Clausen T / Saibil HR | |||||||||
![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 611.8 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.8 KB 12.8 KB | Display Display | ![]() |
Images | ![]() | 216.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 196.8 KB | Display | ![]() |
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Full document | ![]() | 195.9 KB | Display | |
Data in XML | ![]() | 5.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4a8aMC ![]() 1982C ![]() 1983C ![]() 1984C ![]() 4a8bC ![]() 4a8cC ![]() 4a8dC ![]() 4a9gC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Asymmetric cryo-EM map of E. coli DegQ 12-mer in complex with lysozyme | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Escherichia coli DegQ Gallus gallus lysozyme
Entire | Name: Escherichia coli DegQ Gallus gallus lysozyme |
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Components |
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-Supramolecule #1000: Escherichia coli DegQ Gallus gallus lysozyme
Supramolecule | Name: Escherichia coli DegQ Gallus gallus lysozyme / type: sample / ID: 1000 Oligomeric state: Six lysozyme monomers bind to one DegQ 12-mer Number unique components: 2 |
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Molecular weight | Experimental: 625 KDa / Theoretical: 625 KDa Method: Native mass spectrometry Size elution chromatography |
-Macromolecule #1: DegQ
Macromolecule | Name: DegQ / type: protein_or_peptide / ID: 1 / Name.synonym: DegQ / Number of copies: 12 / Oligomeric state: Dodecamer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 45 KDa / Theoretical: 45 KDa |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #2: Lysozyme
Macromolecule | Name: Lysozyme / type: protein_or_peptide / ID: 2 / Name.synonym: Lysozyme / Number of copies: 6 / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Experimental: 14.3 KDa / Theoretical: 14.3 KDa |
Sequence | GO: lysozyme activity / InterPro: Glycoside hydrolase, family 23 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 / Details: 20 mM HEPES/NaOH, 150 mM NaCl |
Grid | Details: C-flat grids (CF-2/2-4C-100 Protochips) |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual plunger / Method: Blot for 2 seconds before plunging |
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Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Min: 90 K / Max: 92 K / Average: 91 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 150,000 times magnification Legacy - Electron beam tilt params: 0 |
Details | Low dose mode |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 100 / Average electron dose: 15 e/Å2 / Bits/pixel: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Single tilt cryo / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Phase flipping |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-5, SPIDER / Number images used: 13432 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
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Software | Name: Chimera, Flex-EM |
Details | PDBEntryID_givenInChain. Protocol: Rigid body and flexible fitting. Protease and PDZ1 trimers extracted from 3STJ pdb entry. PDZ2 domain modelled with MODELLER from E. coli DegP pdb entry 3CS0. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation, energy |
Output model | ![]() PDB-4a8a: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Flex-EM |
Details | PDBEntryID_givenInChain. Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation, energy |
Output model | ![]() PDB-4a8a: |