6N1Q

Dihedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in D2 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.16 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

CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage.

Soczek, K.M.Grant, T.Rosenthal, P.B.Mondragon, A.

(2018) Elife 7

  • DOI: https://doi.org/10.7554/eLife.41215
  • Primary Citation of Related Structures:  
    6N1P, 6N1Q, 6N1R

  • PubMed Abstract: 

    Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.2 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.


  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit A
A, B, C, D, E
A, B, C, D, E, F, G, H
511Streptococcus pneumoniae G54Mutation(s): 0 
Gene Names: gyrA_1gyrAERS409327_01712
EC: 5.99.1.3
UniProt
Find proteins for Q8DPM2 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DPM2 
Go to UniProtKB:  Q8DPM2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DPM2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTREFMAC5
MODEL REFINEMENTPHENIX1.12-2829

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM051350
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35-GM118108
Cancer Research UKUnited KingdomFC001143
Medical Research Council (MRC, United Kingdom)United KingdomFC001143
Wellcome TrustUnited KingdomFC001143

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Refinement description