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Yorodumi- EMDB-1982: Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1982 | |||||||||
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Title | Symmetrized cryo-EM reconstruction of E. coli DegQ 12-mer in complex with lysozymes | |||||||||
Map data | Symmetrized cryo-EM map of Escherichia coli DegQ 12-mer in complex with lysozymes | |||||||||
Sample |
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Keywords | Chaperone / Protease | |||||||||
Function / homology | Function and homology information peptidase Do / 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 Do / 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 / serine-type endopeptidase activity / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Gallus gallus (chicken) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | |||||||||
Authors | Malet H / Canellas F / Sawa J / Yan J / Thalassinos K / Ehrmann M / Clausen T / Saibil HR | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1982.map.gz | 939 KB | EMDB map data format | |
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Header (meta data) | emd-1982-v30.xml emd-1982.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
Images | emd-1982.tif | 219.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1982 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1982 | HTTPS FTP |
-Validation report
Summary document | emd_1982_validation.pdf.gz | 202.8 KB | Display | EMDB validaton report |
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Full document | emd_1982_full_validation.pdf.gz | 201.9 KB | Display | |
Data in XML | emd_1982_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1982 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1982 | HTTPS FTP |
-Related structure data
Related structure data | 4a8bMC 1981C 1983C 1984C 4a8aC 4a8cC 4a8dC 4a9gC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_1982.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Symmetrized cryo-EM map of Escherichia coli DegQ 12-mer in complex with lysozymes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Escherichia coli DegQ 12-mer in complex with lysozyme substrates
Entire | Name: Escherichia coli DegQ 12-mer in complex with lysozyme substrates |
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Components |
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-Supramolecule #1000: Escherichia coli DegQ 12-mer in complex with lysozyme substrates
Supramolecule | Name: Escherichia coli DegQ 12-mer in complex with lysozyme substrates type: sample / ID: 1000 / Details: - Oligomeric state: Six lysozyme monomers bound 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 exclusion 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: Escherichia coli (E. coli) / Strain: K-12 / Location in cell: Periplasm |
Molecular weight | Experimental: 45 KDa / Theoretical: 45 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET26b |
-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: Gallus gallus (chicken) / synonym: Chicken / Tissue: Egg white |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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 / 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: FIELD EMISSION GUN |
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 |
-Image processing
CTF correction | Details: Phase flipping |
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Final reconstruction | Applied symmetry - Point group: T (tetrahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 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 pdb entry 3STJ. |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation, energy |
Output model | PDB-4a8b: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: MODELLER, Chimera, Flex-EM |
Details | Protocol: Rigid body fitting. PDZ2 domain modelled with MODELLER. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation, energy |
Output model | PDB-4a8b: |
-Atomic model buiding 3
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-4a8b: |