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- EMDB-19777: M. tuberculosis gyrase holocomplex with 150 bp DNA and gepotidacin -

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Basic information

Entry
Database: EMDB / ID: EMD-19777
TitleM. tuberculosis gyrase holocomplex with 150 bp DNA and gepotidacin
Map data
Sample
  • Complex: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and Gepotidacin
    • Complex: DNA gyrase
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: DNA
      • DNA: DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')
      • DNA: DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: (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
KeywordsMycobacterium tuberculosis / DNA gyrase / Novel Bacterial Topoisomerase II Inhibitors / antibiotic resistance / structure-activity relation / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) 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) complex / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) 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 / 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 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 gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMechaly A / Gubellini F / Yab E / Willand N / Petrella S / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E ...Mechaly A / Gubellini F / Yab E / Willand N / Petrella S / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E / Wehenkel AM / Alzari PM / Deprez B / Baulard A / Aubry A
Funding support France, 3 items
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 gepotidacin
Authors: Gedeon A / Yab E / Dinut A / Sadowski E / Capton E / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E / Wehenkel AM / Gubellini F / Mechaly A / Alzari PM / Deprez B / Baulard A / Aubry ...Authors: Gedeon A / Yab E / Dinut A / Sadowski E / Capton E / Dreneau A / Gioia B / Piveteau C / Djaout K / Lecat E / Wehenkel AM / Gubellini F / Mechaly A / Alzari PM / Deprez B / Baulard A / Aubry A / Willand N / Petrella S
History
DepositionMar 1, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19777.png

Downloads & links

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Map

FileDownload / File: emd_19777.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å		0.86 Å/pix.
x 384 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.212
Minimum - Maximum-0.4035165 - 0.9844927
Average (Standard dev.)0.00031314197 (±0.021093024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_19777_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19777_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19777_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and Gepot...

EntireName: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and Gepotidacin
Components
  • Complex: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and Gepotidacin
    • Complex: DNA gyrase
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: DNA
      • DNA: DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')
      • DNA: DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')
  • Ligand: MAGNESIUM ION
  • Ligand: (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

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Supramolecule #1: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and Gepot...

SupramoleculeName: Cryo-EM structure of Mtb DNA Gyrase in complex with DNA and Gepotidacin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 430 KDa

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Supramolecule #2: DNA gyrase

SupramoleculeName: DNA gyrase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DNA gyrase subunit A

MacromoleculeName: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 92.30418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TDTTLPPDDS LDRIEPVDIE QEMQRSYIDY AMSVIVGRAL PEVRDGLKPV HRRVLYAMFD SGFRPDRSHA KSARSVAETM GNYHPHGDA SIYDSLVRMA QPWSLRYPLV DGQGNFGSPG NDPPAAMRYT EARLTPLAME MLREIDEETV DFIPNYDGRV Q EPTVLPSR ...String:
TDTTLPPDDS LDRIEPVDIE QEMQRSYIDY AMSVIVGRAL PEVRDGLKPV HRRVLYAMFD SGFRPDRSHA KSARSVAETM GNYHPHGDA SIYDSLVRMA QPWSLRYPLV DGQGNFGSPG NDPPAAMRYT EARLTPLAME MLREIDEETV DFIPNYDGRV Q EPTVLPSR FPNLLANGSG GIAVGMATNI PPHNLRELAD AVFWALENHD ADEEETLAAV MGRVKGPDFP TAGLIVGSQG TA DAYKTGR GSIRMRGVVE VEEDSRGRTS LVITELPYQV NHDNFITSIA EQVRDGKLAG ISNIEDQSSD RVGLRIVIEI KRD AVAKVV INNLYKHTQL QTSFGANMLA IVDGVPRTLR LDQLIRYYVD HQLDVIVRRT TYRLRKANER AHILRGLVKA LDAL DEVIA LIRASETVDI ARAGLIELLD IDEIQAQAIL DMQLRRLAAL ERQRIIDDLA KIEAEIADLE DILAKPERQR GIVRD ELAE IVDRHGDDRR TRIIAIDGDV SDEDLIARED VVVTITETGY AKRTKTDLYR SQKRGGKGVQ GAGLKQDDIV AHFFVC STH DLILFFTTQG RVYRAKAYDL PEASRTARGQ HVANLLAFQP EERIAQVIQI RGYTDAPYLV LATRNGLVKK SKLTDFD SN RSGGIVAVNL RDNDELVGAV LCSAGDDLLL VSANGQSIRF SATDEALRPM GRATSGVQGM RFNIDDRLLS LNVVREGT Y LLVATSGGYA KRTAIEEYPV QGRGGKGVLT VMYDRRRGRL VGALIVDDDS ELYAVTSGGG VIRTAARQVR KAGRQTKGV RLMNLGEGDT LLAIARNAEE SGDDNAVDAN GADQTGN

UniProtKB: DNA gyrase subunit A

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Macromolecule #2: DNA gyrase subunit B

MacromoleculeName: DNA gyrase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing)
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 74.423953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMVAAQKKK AQDEYGAASI TILEGLEAVR KRPGMYIGST GERGLHHLIW EVVDNAVDEA MAGYATTVNV VLLEDGGVEV ADDGRGIPV ATHASGIPTV DVVMTQLHAG GKFDSDAYAI SGGLHGVGVS VVNALSTRLE VEIKRDGYEW SQVYEKSEPL G LKQGAPTK ...String:
GAMVAAQKKK AQDEYGAASI TILEGLEAVR KRPGMYIGST GERGLHHLIW EVVDNAVDEA MAGYATTVNV VLLEDGGVEV ADDGRGIPV ATHASGIPTV DVVMTQLHAG GKFDSDAYAI SGGLHGVGVS VVNALSTRLE VEIKRDGYEW SQVYEKSEPL G LKQGAPTK KTGSTVRFWA DPAVFETTEY DFETVARRLQ EMAFLNKGLT INLTDERVTQ DEVVDEVVSD VAEAPKSASE RA AESTAPH KVKSRTFHYP GGLVDFVKHI NRTKNAIHSS IVDFSGKGTG HEVEIAMQWN AGYSESVHTF ANTINTHEGG THE EGFRSA LTSVVNKYAK DRKLLKDKDP NLTGDDIREG LAAVISVKVS EPQFEGQTKT KLGNTEVKSF VQKVCNEQLT HWFE ANPTD AKVVVNKAVS SAQARIAARK ARELVRRKSA TDIGGLPGKL ADCRSTDPRK SELYVVEGDS AGGSAKSGRD SMFQA ILPL RGKIINVEKA RIDRVLKNTE VQAIITALGT GIHDEFDIGK LRYHKIVLMA DADVDGQHIS TLLLTLLFRF MRPLIE NGH VFLAQPPLYK LKWQRSDPEF AYSDRERDGL LEAGLKAGKK INKEDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVT LD DAAAADELFS ILMGEDVDAR RSFITRNAKD VRFLDV

UniProtKB: DNA gyrase subunit B

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Macromolecule #3: DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')

MacromoleculeName: DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')
type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.325371 KDa
SequenceString: (DG)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DC)(DG) (DT)(DT)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DT) (DA)(DG)(DG)(DG)(DC)(DT)(DA)(DC)(DG) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DG) (DC) (DT)(DC)(DT)(DT)(DC)(DT) ...String:
(DG)(DT)(DA)(DC)(DC)(DG)(DG)(DA)(DC)(DG) (DT)(DT)(DG)(DC)(DG)(DC)(DC)(DC)(DG)(DT) (DA)(DG)(DG)(DG)(DC)(DT)(DA)(DC)(DG) (DG)(DC)(DG)(DG)(DC)(DC)(DT)(DT)(DC)(DG) (DC) (DT)(DC)(DT)(DT)(DC)(DT)(DT)(DA) (DG)(DT)(DA)(DT)(DT)(DA)(DC)(DC)(DC)(DC) (DT)(DT) (DC)(DC)(DG)(DG)(DT)(DA)(DG) (DG)(DT)(DC)(DG)(DG)(DA)(DG)(DC)(DG)(DC) (DA)(DG)(DC) (DG)(DC)(DT)(DT)(DG)(DC) (DG)(DG)(DT)(DC)(DG)(DT)(DT)(DC)(DT)(DG) (DC)(DA)(DT)(DC) (DG)(DG)(DG)(DT)(DC) (DG)(DC)(DG)(DC)(DA)(DG)(DC)(DC)(DG)(DG) (DC)(DG)(DG)(DT)(DA) (DC)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DA)(DT)(DT)(DA)(DC)(DC) (DG)(DG)(DA)(DC)(DG)(DA) (DA)(DG)(DA) (DG)(DC)(DG)(DG)(DC)(DT)(DT)

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Macromolecule #4: DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')

MacromoleculeName: DNA (5'-D(*AP*GP*TP*AP*TP*TP*AP*CP*CP*CP*CP*TP*TP*CP*CP*GP*GP*A)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.29148 KDa
SequenceString: (DA)(DA)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DT) (DT)(DC)(DG)(DT)(DC)(DC)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DT)(DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG) (DC) (DT)(DG)(DC)(DG)(DC)(DG) ...String:
(DA)(DA)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DT) (DT)(DC)(DG)(DT)(DC)(DC)(DG)(DG)(DT)(DA) (DA)(DT)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DG)(DT)(DA)(DC)(DC)(DG)(DC)(DC)(DG)(DG) (DC) (DT)(DG)(DC)(DG)(DC)(DG)(DA)(DC) (DC)(DC)(DG)(DA)(DT)(DG)(DC)(DA)(DG)(DA) (DA)(DC) (DG)(DA)(DC)(DC)(DG)(DC)(DA) (DA)(DG)(DC)(DG)(DC)(DT)(DG)(DC)(DG)(DC) (DT)(DC)(DC) (DG)(DA)(DC)(DC)(DT)(DA) (DC)(DC)(DG)(DG)(DA)(DA)(DG)(DG)(DG)(DG) (DT)(DA)(DA)(DT) (DA)(DC)(DT)(DA)(DA) (DG)(DA)(DA)(DG)(DA)(DG)(DC)(DG)(DA)(DA) (DG)(DG)(DC)(DC)(DG) (DC)(DC)(DG)(DT) (DA)(DG)(DC)(DC)(DC)(DT)(DA)(DC)(DG)(DG) (DG)(DC)(DG)(DC)(DA)(DA) (DC)(DG)(DT) (DC)(DC)(DG)(DG)(DT)(DA)(DC)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethyla...

MacromoleculeName: (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
type: ligand / ID: 6 / Number of copies: 1 / Formula: JHN
Molecular weightTheoretical: 448.518 Da
Chemical component information

ChemComp-JHN:
(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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 830271
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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