[English] 日本語
Yorodumi- EMDB-4913: CryoEM structure of the complete E. coli DNA Gyrase complex bound... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4913 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex | ||||||||||||
Map data | The complete E. coli DNA Gyrase complex | ||||||||||||
Sample |
| ||||||||||||
Keywords | Isomerase / Complex / DNA Gyrase / Inhibitor / DNA BINDING PROTEIN | ||||||||||||
Function / homology | Function and homology information negative regulation of DNA-templated DNA replication / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus ...negative regulation of DNA-templated DNA replication / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / identical protein binding / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Escherichia coli K-12 (bacteria) / Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.6 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_4913.map.gz | 16.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-4913-v30.xml emd-4913.xml | 21.1 KB 21.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4913_fsc.xml | 12.7 KB | Display | FSC data file |
Images | emd_4913.png | 53.7 KB | ||
Masks | emd_4913_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-4913.cif.gz | 7.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4913 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4913 | HTTPS FTP |
-Related structure data
Related structure data | 6rkwMC 4909C 4910C 4912C 4914C 4915C 6rksC 6rkuC 6rkvC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_4913.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | The complete E. coli DNA Gyrase complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_4913_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : The complete E. coli DNA Gyrase complex bound to 130bp DNA duplex
+Supramolecule #1: The complete E. coli DNA Gyrase complex bound to 130bp DNA duplex
+Supramolecule #2: DNA gyrase subunit A
+Supramolecule #3: DNA gyrase subunit B
+Supramolecule #4: DNA
+Macromolecule #1: DNA gyrase subunit A
+Macromolecule #2: DNA gyrase subunit B
+Macromolecule #3: DNA (58-MER)
+Macromolecule #4: DNA (62-MER)
+Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #6: (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethyla...
-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 |
+Image processing
-Atomic model buiding 1
Initial model |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Space: REAL | ||||||||||||||||
Output model | PDB-6rkw: |