+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4915 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | E. coli DNA Gyrase - CTD & DNA binding and cleavage domain | ||||||||||||
Map data | E. coli DNA Gyrase - CTD and DNA binding and cleavage domain | ||||||||||||
Sample |
| ||||||||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 Å | ||||||||||||
Authors | Vanden Broeck A / Lamour V | ||||||||||||
Funding support | France, 3 items
| ||||||||||||
Citation | Journal: Nat Commun / Year: 2019 Title: Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Authors: Arnaud Vanden Broeck / Christophe Lotz / Julio Ortiz / Valérie Lamour / Abstract: DNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of ...DNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of the full-length DNA gyrase from the model organism E. coli is still missing. Herein, we report the complete structure of the E. coli DNA gyrase nucleoprotein complex trapped by the antibiotic gepotidacin, using phase-plate single-particle cryo-electron microscopy. Our data unveil the structural and spatial organization of the functional domains, their connections and the position of the conserved GyrA-box motif. The deconvolution of two states of the DNA-binding/cleavage domain provides a better understanding of the allosteric movements of the enzyme complex. The local atomic resolution in the DNA-bound area reaching up to 3.0 Å enables the identification of the antibiotic density. Altogether, this study paves the way for the cryo-EM determination of gyrase complexes with antibiotics and opens perspectives for targeting conformational intermediates. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4915.map.gz | 11 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4915-v30.xml emd-4915.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4915_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_4915.png | 55.8 KB | ||
Masks | emd_4915_msk_1.map | 178 MB | Mask map | |
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4915 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4915 | HTTPS FTP |
-Validation report
Summary document | emd_4915_validation.pdf.gz | 247.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_4915_full_validation.pdf.gz | 246.9 KB | Display | |
Data in XML | emd_4915_validation.xml.gz | 13 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4915 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4915 | HTTPS FTP |
-Related structure data
Related structure data | 4909C 4910C 4912C 4913C 4914C 6rksC 6rkuC 6rkvC 6rkwC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_4915.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | E. coli DNA Gyrase - CTD and DNA binding and cleavage domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_4915_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : CTD & DNA binding and cleavage domains of the E. coli DNA Gyrase
Entire | Name: CTD & DNA binding and cleavage domains of the E. coli DNA Gyrase |
---|---|
Components |
|
-Supramolecule #1: CTD & DNA binding and cleavage domains of the E. coli DNA Gyrase
Supramolecule | Name: CTD & DNA binding and cleavage domains of the E. coli DNA Gyrase type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 3-40 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 0.8 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 130000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |