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- PDB-36yd: S. aureus DNA Gyrase in complex with OSUAB-0276 and DNA -

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Basic information

Entry
Database: PDB / ID: 36yd
TitleS. aureus DNA Gyrase in complex with OSUAB-0276 and DNA
Components
  • DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
  • DNA gyrase subunit B,DNA gyrase subunit A
KeywordsDNA BINDING PROTEIN / Topoisomerase / NBTI
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / cytoplasm
Similarity search - Function
DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / : / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus ...DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / : / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus N315 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsWheat, C.T. / Bell, C.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI173072 United States
CitationJournal: To Be Published
Title: OSUAB-0276, a novel bacterial topoisomerase inhibitor (NBTI) with dual activity against bacterial and human type II topoisomerases
Authors: Cassel, S.R. / Powell, J.W. / Wheat, C.T. / Tomaszewski, A.J. / Dellos-Nolan, S. / Landgraf, A.D. / Sham, M.P. / Carvajal-Moreno, J. / Lu, Y. / Chen, A. / Bell, C.E. / Wozniak, D.J. / ...Authors: Cassel, S.R. / Powell, J.W. / Wheat, C.T. / Tomaszewski, A.J. / Dellos-Nolan, S. / Landgraf, A.D. / Sham, M.P. / Carvajal-Moreno, J. / Lu, Y. / Chen, A. / Bell, C.E. / Wozniak, D.J. / Yalowich, J.C. / Mitton-Fry, M.J.
History
DepositionJul 6, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
D: DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')
A: DNA gyrase subunit B,DNA gyrase subunit A
B: DNA gyrase subunit B,DNA gyrase subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,2177
Polymers168,6044
Non-polymers6133
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: DNA chain DNA (5'-D(P*AP*GP*CP*CP*GP*TP*AP*GP*GP*GP*CP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 6135.955 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein DNA gyrase subunit B,DNA gyrase subunit A


Mass: 78166.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus N315 (bacteria)
Gene: gyrB, SA0005, gyrA, SA0006 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P66937, UniProt: Q99XG5, DNA topoisomerase (ATP-hydrolysing)
#3: Chemical ChemComp-A1DMB / (6P)-6-(1-{1-[2-(3-fluoro-6-methoxy-1,5-naphthyridin-4-yl)ethyl]piperidin-4-yl}-1H-1,2,3-triazol-4-yl)-2H-1,4-benzoxazin-3(4H)-one


Mass: 503.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26FN7O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: S. aureus DNA Gyrase in complex with OSUAB-0276 and DNA
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Staphylococcus aureus subsp. aureus N315 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272000 / Symmetry type: POINT
RefinementHighest resolution: 2.68 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00511772
ELECTRON MICROSCOPYf_angle_d1.0316040
ELECTRON MICROSCOPYf_dihedral_angle_d14.421942
ELECTRON MICROSCOPYf_chiral_restr0.061800
ELECTRON MICROSCOPYf_plane_restr0.0141964

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