6RKU

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    6RKS, 6RKU, 6RKV, 6RKW

  • 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. coli is still missing ...

    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: 

    Hôpitaux Universitaires de Strasbourg, 1 Place de l'Hôpital, 67091, Strasbourg Cedex, France. lamourv@igbmc.fr.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit AA, C875Escherichia coli K-12Mutation(s): 0 
Gene Names: gyrA, hisW, nalA, parD, b2231, JW2225
EC: 5.6.2.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0AES4 (Escherichia coli (strain K12))
Explore P0AES4 
Go to UniProtKB:  P0AES4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AES4
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BB, D804Escherichia coli K-12Mutation(s): 0 
Gene Names: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625
EC: 5.6.2.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12))
Explore P0AES6 
Go to UniProtKB:  P0AES6
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UniProt GroupP0AES6
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA Strand 1F [auth E],
E [auth F]		14Escherichia coli
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA Strand 2G, H 18Escherichia coli
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JHN
Query on JHN
Download Ideal Coordinates CCD File 
I [auth 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: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2020-11-18
    Changes: Data collection