6RKU

E. coli DNA Gyrase - DNA binding and cleavage domain in State 1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.

Vanden Broeck, A., Lotz, C., Ortiz, J., Lamour, V.

(2019) Nat Commun 10: 4935-4935

  • DOI: 10.1038/s41467-019-12914-y
  • Primary Citation of Related Structures:  

  • PubMed 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 the full-length DNA gyrase from the model organism E ...

    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.

    Organizational Affiliation: 

    Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. lamourv@igbmc.fr.,Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France. lamourv@igbmc.fr.,Université de Strasbourg, Illkirch, France. lamourv@igbmc.fr.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Hôpitaux Universitaires de Strasbourg, 1 Place de l'Hôpital, 67091, Strasbourg Cedex, France. lamourv@igbmc.fr.,Université de Strasbourg, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France. lamourv@igbmc.fr.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, C
875Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gyrA (hisW, nalA, parD)
EC: 5.6.2.2
Find proteins for P0AES4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AES4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
B, D
804Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gyrB (acrB, cou, himB, hisU, nalC, parA, pcbA)
EC: 5.6.2.2
Find proteins for P0AES6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AES6
Entity ID: 3
MoleculeChainsLengthOrganism
DNA Strand 1F,E14Escherichia coli
Entity ID: 4
MoleculeChainsLengthOrganism
DNA Strand 2G,H18Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JHN
Query on JHN
Download SDF File 
Download CCD File 
G
(3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione
C24 H28 N6 O3
PZFAZQUREQIODZ-LJQANCHMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-LABX-0030-INRT
French National Research AgencyFranceANR-10-IDEX-0002-02
French Infrastructure for Integrated Structural BiologyFranceFRISBI ANR-10-INBS-05

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Type: Data collection, Database references