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- EMDB-51339: E.coli gyrase holocomplex with cleaved chirally wrapped 217 bp DN... -

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Entry
Database: EMDB / ID: EMD-51339
TitleE.coli gyrase holocomplex with cleaved chirally wrapped 217 bp DNA fragment and moxifloxacin
Map data
Sample
  • Complex: Ternary complex of Escherichia coli DNA gyrase with 217 bp linear DNA fragment and moxifloxacin
    • Protein or peptide: DNA gyrase subunit A
    • Protein or peptide: DNA gyrase subunit B
    • DNA: Mu217R
    • DNA: Mu217F
  • Ligand: MAGNESIUM ION
  • Ligand: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
  • Ligand: water
KeywordsDNA gyrase / type II topoisomerase / moxifloxacin / DNA crossover / ISOMERASE
Function / homology
Function and homology information


negative regulation of DNA-templated DNA replication / 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 / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus ...negative regulation of DNA-templated DNA replication / 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 / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / 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 ...: / GyrB, hook / DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / 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 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA gyrase subunit A / DNA gyrase subunit B
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia phage Mu (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGhilarov D / Heddle JG / Pabis M
Funding support United Kingdom, Poland, 3 items
OrganizationGrant numberCountry
Wellcome Trust221868/Z/20/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X01097X/1 United Kingdom
Polish National Science Centre2020/39/B/NZ1/02898 Poland
CitationJournal: Proc Natl Acad Sci U S A / Year: 2024
Title: Structural basis of chiral wrap and T-segment capture by DNA gyrase.
Authors: Elizabeth Michalczyk / Zuzanna Pakosz-Stępień / Jonathon D Liston / Olivia Gittins / Marta Pabis / Jonathan G Heddle / Dmitry Ghilarov /
Abstract: Type II topoisomerase DNA gyrase transduces the energy of ATP hydrolysis into the negative supercoiling of DNA. The postulated catalytic mechanism involves stabilization of a chiral DNA loop followed ...Type II topoisomerase DNA gyrase transduces the energy of ATP hydrolysis into the negative supercoiling of DNA. The postulated catalytic mechanism involves stabilization of a chiral DNA loop followed by the passage of the T-segment through the temporarily cleaved G-segment resulting in sign inversion. The molecular basis for this is poorly understood as the chiral loop has never been directly observed. We have obtained high-resolution cryoEM structures of gyrase with chirally wrapped 217 bp DNA with and without the fluoroquinolone moxifloxacin (MFX). Each structure constrains a positively supercoiled figure-of-eight DNA loop stabilized by a GyrA β-pinwheel domain which has the structure of a flat disc. By comparing the catalytic site of the native drug-free and MFX-bound gyrase structures both of which contain a single metal ion, we demonstrate that the enzyme is observed in a native precatalytic state. Our data imply that T-segment trapping is not dependent on the dimerization of the ATPase domains which appears to only be possible after strand passage has taken place.
History
DepositionAug 13, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51339.png

Downloads & links

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Map

FileDownload / File: emd_51339.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.118051656 - 0.36253735
Average (Standard dev.)0.00015267728 (±0.005863453)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51339_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51339_half_map_2.map
Projections & Slices
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Sample components

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Entire : Ternary complex of Escherichia coli DNA gyrase with 217 bp linear...

EntireName: Ternary complex of Escherichia coli DNA gyrase with 217 bp linear DNA fragment and moxifloxacin
Components
  • Complex: Ternary complex of Escherichia coli DNA gyrase with 217 bp linear DNA fragment and moxifloxacin
    • Protein or peptide: DNA gyrase subunit A
    • Protein or peptide: DNA gyrase subunit B
    • DNA: Mu217R
    • DNA: Mu217F
  • Ligand: MAGNESIUM ION
  • Ligand: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
  • Ligand: water

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Supramolecule #1: Ternary complex of Escherichia coli DNA gyrase with 217 bp linear...

SupramoleculeName: Ternary complex of Escherichia coli DNA gyrase with 217 bp linear DNA fragment and moxifloxacin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Escherichia coli (E. coli)

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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: Escherichia coli (E. coli) / Strain: MG1655
Molecular weightTheoretical: 97.854305 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTI VRMAQPFSLR YMLVDGQGNF GSIDGDSAAA MR(PTR)TEIRLAK IAHELMADLE KETVDFVDNY DGTEKIP DV MPTKIPNLLV ...String:
SSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTI VRMAQPFSLR YMLVDGQGNF GSIDGDSAAA MR(PTR)TEIRLAK IAHELMADLE KETVDFVDNY DGTEKIP DV MPTKIPNLLV NGSSGIAVGM ATNIPPHNLT EVINGCLAYI DDEDISIEGL MEHIPGPDFP TAAIINGRRG IEEAYRTG R GKVYIRARAE VEVDAKTGRE TIIVHEIPYQ VNKARLIEKI AELVKEKRVE GISALRDESD KDGMRIVIEV KRDAVGEVV LNNLYSQTQL QVSFGINMVA LHHGQPKIMN LKDIIAAFVR HRREVVTRRT IFELRKARDR AHILEALAVA LANIDPIIEL IRHAPTPAE AKTALVANPW QLGNVAAMLE RAGDDAARPE WLEPEFGVRD GLYYLTEQQA QAILDLRLQK LTGLEHEKLL D EYKELLDQ IAELLRILGS ADRLMEVIRE ELELVREQFG DKRRTEITAN SADINLEDLI TQEDVVVTLS HQGYVKYQPL SE YEAQRRG GKGKSAARIK EEDFIDRLLV ANTHDHILCF SSRGRVYSMK VYQLPEATRG ARGRPIVNLL PLEQDERITA ILP VTEFEE GVKVFMATAN GTVKKTVLTE FNRLRTAGKV AIKLVDGDEL IGVDLTSGED EVMLFSAEGK VVRFKESSVR AMGC NTTGV RGIRLGEGDK VVSLIVPRGD GAILTATQNG YGKRTAVAEY PTKSRATKGV ISIKVTERNG LVVGAVQVDD CDQIM MITD AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA EPVDEEDLDT IDGSAAEGDD EIAPEVDVDD EPEEEL EVL FQ

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: Escherichia coli (E. coli) / Strain: MG1655
Molecular weightTheoretical: 90.891734 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPSNSYDSSS IKVLKGLDAV RKRPGMYIGD TDDGTGLHHM VFEVVDNAID EALAGHCKEI IVTIHADNSV SVQDDGRGIP TGIHPEEGV SAAEVIMTVL HAGGKFDDNS YKVSGGLHGV GVSVVNALSQ KLELVIQREG KIHRQIYEHG VPQAPLAVTG E TEKTGTMV ...String:
GPSNSYDSSS IKVLKGLDAV RKRPGMYIGD TDDGTGLHHM VFEVVDNAID EALAGHCKEI IVTIHADNSV SVQDDGRGIP TGIHPEEGV SAAEVIMTVL HAGGKFDDNS YKVSGGLHGV GVSVVNALSQ KLELVIQREG KIHRQIYEHG VPQAPLAVTG E TEKTGTMV RFWPSLETFT NVTEFEYEIL AKRLRELSFL NSGVSIRLRD KRDGKEDHFH YEGGIKAFVE YLNKNKTPIH PN IFYFSTE KDGIGVEVAL QWNDGFQENI YCFTNNIPQR DGGTHLAGFR AAMTRTLNAY MDKEGYSKKA KVSATGDDAR EGL IAVVSV KVPDPKFSSQ TKDKLVSSEV KSAVEQQMNE LLAEYLLENP TDAKIVVGKI IDAARAREAA RRAREMTRRK GALD LAGLP GKLADCQERD PALSELYLVE GDSAGGSAKQ GRNRKNQAIL PLKGKILNVE KARFDKMLSS QEVATLITAL GCGIG RDEY NPDKLRYHSI IIMTDADVDG SHIRTLLLTF FYRQMPEIVE RGHVYIAQPP LYKVKKGKQE QYIKDDEAMD QYQISI ALD GATLHTNASA PALAGEALEK LVSEYNATQK MINRMERRYP KAMLKELIYQ PTLTEADLSD EQTVTRWVNA LVSELND KE QHGSQWKFDV HTNAEQNLFE PIVRVRTHGV DTDYPLDHEF ITGGEYRRIC TLGEKLRGLL EEDAFIERGE RRQPVASF E QALDWLVKES RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL MGDAVEPRRA FIEENALKA ANIDIENLYF Q

UniProtKB: DNA gyrase subunit B

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Macromolecule #3: Mu217R

MacromoleculeName: Mu217R / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 65.926109 KDa
SequenceString: (DT)(DT)(DC)(DC)(DT)(DG)(DC)(DG)(DC)(DG) (DT)(DC)(DC)(DT)(DT)(DA)(DT)(DA)(DT)(DG) (DG)(DG)(DG)(DC)(DT)(DG)(DG)(DA)(DT) (DA)(DA)(DG)(DA)(DC)(DC)(DG)(DG)(DG)(DG) (DA) (DA)(DC)(DA)(DG)(DG)(DA) ...String:
(DT)(DT)(DC)(DC)(DT)(DG)(DC)(DG)(DC)(DG) (DT)(DC)(DC)(DT)(DT)(DA)(DT)(DA)(DT)(DG) (DG)(DG)(DG)(DC)(DT)(DG)(DG)(DA)(DT) (DA)(DA)(DG)(DA)(DC)(DC)(DG)(DG)(DG)(DG) (DA) (DA)(DC)(DA)(DG)(DG)(DA)(DA)(DA) (DT)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DG)(DC) (DC)(DA) (DT)(DC)(DA)(DG)(DA)(DA)(DA) (DA)(DC)(DG)(DC)(DG)(DT)(DC)(DA)(DG)(DC) (DG)(DC)(DC) (DG)(DC)(DT)(DC)(DT)(DG) (DA)(DG)(DG)(DC)(DA)(DA)(DT)(DA)(DA)(DA) (DC)(DA)(DG)(DA) (DA)(DT)(DC)(DA)(DG) (DG)(DC)(DA)(DT)(DA)(DA)(DA)(DA)(DT)(DC) (DA)(DC)(DC)(DC)(DG) (DC)(DA)(DC)(DA) (DG)(DA)(DT)(DT)(DT)(DT)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG) (DC)(DC)(DA) (DC)(DG)(DG)(DG)(DA)(DT)(DT)(DT)(DT)(DT) (DA)(DA)(DA)(DC)(DC)(DG)(DG) (DT)(DA) (DT)(DT)(DT)(DA)(DA)(DC)(DG)(DG)(DT)(DG) (DT)(DA)(DT)(DG)(DA)(DA)(DT)(DC) (DC) (DC)(DG)(DT)(DT)(DT)(DT)(DA)(DT)(DC)(DT) (DT)(DC)(DC)(DT)(DT)(DT)(DC)(DA)(DC) (DT)(DT)(DT)(DC)(DT)(DT)(DT)(DC)(DT)(DC) (DC)(DA)(DG)(DT)

GENBANK: GENBANK: M74911.1

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Macromolecule #4: Mu217F

MacromoleculeName: Mu217F / type: dna / ID: 4 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Escherichia phage Mu (virus)
Molecular weightTheoretical: 66.202258 KDa
SequenceString: (DA)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DA) (DG)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DA)(DA) (DG)(DG)(DA)(DA)(DG)(DA)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC) (DA) (DT)(DA)(DC)(DA)(DC)(DC) ...String:
(DA)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DA) (DG)(DA)(DA)(DA)(DG)(DT)(DG)(DA)(DA)(DA) (DG)(DG)(DA)(DA)(DG)(DA)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DC) (DA) (DT)(DA)(DC)(DA)(DC)(DC)(DG)(DT) (DT)(DA)(DA)(DA)(DT)(DA)(DC)(DC)(DG)(DG) (DT)(DT) (DT)(DA)(DA)(DA)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DT)(DG)(DG)(DC)(DG)(DC) (DG)(DT)(DT) (DT)(DT)(DA)(DA)(DA)(DA) (DA)(DA)(DT)(DC)(DT)(DG)(DT)(DG)(DC)(DG) (DG)(DG)(DT)(DG) (DA)(DT)(DT)(DT)(DT) (DA)(DT)(DG)(DC)(DC)(DT)(DG)(DA)(DT)(DT) (DC)(DT)(DG)(DT)(DT) (DT)(DA)(DT)(DT) (DG)(DC)(DC)(DT)(DC)(DA)(DG)(DA)(DG)(DC) (DG)(DG)(DC)(DG)(DC)(DT) (DG)(DA)(DC) (DG)(DC)(DG)(DT)(DT)(DT)(DT)(DC)(DT)(DG) (DA)(DT)(DG)(DG)(DC)(DA)(DT) (DC)(DA) (DA)(DA)(DA)(DA)(DT)(DT)(DT)(DC)(DC)(DT) (DG)(DT)(DT)(DC)(DC)(DC)(DC)(DG) (DG) (DT)(DC)(DT)(DT)(DA)(DT)(DC)(DC)(DA)(DG) (DC)(DC)(DC)(DC)(DA)(DT)(DA)(DT)(DA) (DA)(DG)(DG)(DA)(DC)(DG)(DC)(DG)(DC)(DA) (DG)(DG)(DA)(DA)

GENBANK: GENBANK: M74911.1

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrol...

MacromoleculeName: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
type: ligand / ID: 6 / Number of copies: 2 / Formula: MFX
Molecular weightTheoretical: 401.431 Da
Chemical component information

ChemComp-MFX:
1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.68 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
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: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 79415
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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