+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5290 | |||||||||
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Title | The cryo-EM map of DegQ 12-mer | |||||||||
Map data | This is a cryo-EM map of DegQ 12-mer. | |||||||||
Sample |
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Keywords | HtrA / 12-mer | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
Authors | Bai XC / Wang XJ / Ye YY / Pan XJ / Chang LF / Leng D / Sui SF | |||||||||
Citation | Journal: Structure / Year: 2011 Title: Characterization of the structure and function of Escherichia coli DegQ as a representative of the DegQ-like proteases of bacterial HtrA family proteins. Authors: Xiao-chen Bai / Xi-jiang Pan / Xiao-jing Wang / Yun-ying Ye / Lei-fu Chang / Dong Leng / Jianlin Lei / Sen-Fang Sui / Abstract: HtrA family proteins play a central role in protein quality control in the bacterial periplasmic space. DegQ-like proteases, a group of bacterial HtrA proteins, are characterized by a short LA loop ...HtrA family proteins play a central role in protein quality control in the bacterial periplasmic space. DegQ-like proteases, a group of bacterial HtrA proteins, are characterized by a short LA loop as compared with DegP-like proteases, and are found in many bacterial species. As a representative of the DegQ-like proteases, we report that Escherichia coli DegQ exists in vivo primarily as a trimer (substrate-free) or dodecamer (substrate-containing). Biochemical analysis of DegQ dodecamers revealed that the major copurified protein substrate is OmpA. Importantly, wild-type DegQ exhibited a much lower proteolytic activity, and thus higher chaperone-like activity, than DegP. Furthermore, using cryo-electron microscopy we determined high-resolution structures of DegQ 12- and 24-mers in the presence of substrate, thus revealing the structural mechanism by which DegQ moderates its proteolytic activity. | |||||||||
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_5290.map.gz | 2.7 MB | EMDB map data format | |
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Header (meta data) | emd-5290-v30.xml emd-5290.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | emd_5290_1.jpg | 219.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5290 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5290 | HTTPS FTP |
-Validation report
Summary document | emd_5290_validation.pdf.gz | 79.4 KB | Display | EMDB validaton report |
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Full document | emd_5290_full_validation.pdf.gz | 78.5 KB | Display | |
Data in XML | emd_5290_validation.xml.gz | 491 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5290 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5290 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5290.map.gz / Format: CCP4 / Size: 11.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a cryo-EM map of DegQ 12-mer. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.46 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 : DegQ
Entire | Name: DegQ |
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Components |
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-Supramolecule #1000: DegQ
Supramolecule | Name: DegQ / type: sample / ID: 1000 / Oligomeric state: 12-mer / Number unique components: 12 |
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Molecular weight | Experimental: 500 KDa / Theoretical: 500 KDa / Method: size-exclusion chromatography |
-Macromolecule #1: DegQ
Macromolecule | Name: DegQ / type: protein_or_peptide / ID: 1 / Name.synonym: DegQ / Number of copies: 12 / Oligomeric state: 12-mer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) / synonym: Escherichia coli / Location in cell: periplasmic |
Molecular weight | Experimental: 45 MDa / Theoretical: 45 MDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET-28a |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 7.6 / Details: 40 mM Na2HPO4, 10 mM NaH2PO4, 25 mM NaCl |
Grid | Details: 400 mesh grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Vitrification instrument: Vitrobot Mark IV / Method: Blot for 1.5 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jan 3, 2011 |
Image recording | Category: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 15 µm / Number real images: 315 / Average electron dose: 20 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 102740 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 24604 |
Final two d classification | Number classes: 180 |