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- PDB-8s7o: M. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403 -

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Basic information

Entry
Database: PDB / ID: 8s7o
TitleM. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403
Components
  • (DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')) x 2
  • DNA gyrase subunit A
  • DNA gyrase subunit B
KeywordsDNA BINDING PROTEIN / Mycobacterium tuberculosis / DNA gyrase / Novel Bacterial Topoisomerase II Inhibitors / antibiotic resistance / structure-activity relation
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding ...DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / peptidoglycan-based cell wall / DNA-templated DNA replication / chromosome / response to antibiotic / magnesium ion binding / ATP hydrolysis activity / DNA binding / ATP binding / plasma membrane / 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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 / EF-hand calcium-binding domain. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsGedeon, A. / Yab, E. / Dinut, A. / Sadowski, E. / Capton, E. / Dreneau, A. / Gioia, B. / Piveteau, C. / Djaout, K. / Lecat, E. ...Gedeon, A. / Yab, E. / Dinut, A. / Sadowski, E. / Capton, E. / Dreneau, A. / Gioia, B. / Piveteau, C. / Djaout, K. / Lecat, E. / Wehenkel, A.M. / Gubellini, F. / Mechaly, A. / Alzari, P.M. / Deprez, B. / Baulard, A. / Aubry, A. / Willand, N. / Petrella, S.
Funding support France, 3items
OrganizationGrant numberCountry
IdEx Universite Paris Cite France
Agence Nationale de la Recherche (ANR)ANR-18-IDEX-0001 France
Fondation pour la Recherche Medicale (FRM)EQU202303016284 France
CitationJournal: To Be Published
Title: M. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403
Authors: Gedeon, A. / Yab, E. / Dinut, A. / Sadowski, E. / Capton, E. / Dreneau, A. / Gioia, B. / Piveteau, C. / Djaout, K. / Lecat, E. / Wehenkel, A.M. / Gubellini, F. / Mechaly, A. / Alzari, P.M. / ...Authors: Gedeon, A. / Yab, E. / Dinut, A. / Sadowski, E. / Capton, E. / Dreneau, A. / Gioia, B. / Piveteau, C. / Djaout, K. / Lecat, E. / Wehenkel, A.M. / Gubellini, F. / Mechaly, A. / Alzari, P.M. / Deprez, B. / Baulard, A. / Aubry, A. / Willand, N. / Petrella, S.
History
DepositionMar 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)426,5217
Polymers426,0736
Non-polymers4481
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20010 Å2
ΔGint-113 kcal/mol
Surface area55420 Å2
MethodPISA

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Components

#1: Protein DNA gyrase subunit A / Type IIA topoisomerase subunit GyrA


Mass: 92304.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: gyrA, Rv0006, MTCY10H4.04 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WG47, DNA topoisomerase (ATP-hydrolysing)
#2: Protein DNA gyrase subunit B


Mass: 74423.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: gyrB, Rv0005, MTCY10H4.03 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WG45, DNA topoisomerase (ATP-hydrolysing)
#3: DNA chain DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')


Mass: 46325.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')


Mass: 46291.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-A1H5Q / 6-[[2-[1-(6-methoxy-1,5-naphthyridin-4-yl)-1,2,3-triazol-4-yl]ethylamino]methyl]-4H-1,4-benzothiazin-3-one


Mass: 447.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21N7O2S / Feature type: SUBJECT OF INVESTIGATION
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

Component
IDNameTypeEntity IDParent-IDSource
1Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and BDM71403COMPLEX#1-#40MULTIPLE SOURCES
2DNA gyraseCOMPLEX#1-#21RECOMBINANT
3DNACOMPLEX#3-#41RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Mycobacterium tuberculosis (bacteria)1773
33synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33synthetic construct (others)32630
Buffer solutionpH: 8
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 900 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 987000 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00411496
ELECTRON MICROSCOPYf_angle_d0.6415694
ELECTRON MICROSCOPYf_dihedral_angle_d13.2011833
ELECTRON MICROSCOPYf_chiral_restr0.0411786
ELECTRON MICROSCOPYf_plane_restr0.0041953

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