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- EMDB-51222: E.coli gyrase holocomplex with chirally wrapped 217 bp DNA fragment -

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Basic information

Entry
Database: EMDB / ID: EMD-51222
TitleE.coli gyrase holocomplex with chirally wrapped 217 bp DNA fragment
Map datacomposite map
Sample
  • Complex: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment
    • Complex: E. coli DNA gyrase
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: dsDNA
      • DNA: Mu217 DNA (159-MER)
      • DNA: Mu217 DNA (159-MER)
  • Ligand: MAGNESIUM ION
KeywordsDNA gyrase / type II topoisomerase / supercoiling / DNA crossover / ISOMERASE
Function / homology
Function and homology information


negative regulation of DNA-templated DNA replication / DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / 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 / identical protein binding / membrane / metal ion binding / cytosol / cytoplasm
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 / Topoisomerase (Topo) IIA-type catalytic domain profile. ...: / 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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 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: 2.32 Å
AuthorsMichalczyk E / Ghilarov D
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: Proceedings of the National Academy of Sciences USA
Year: 2024
Title: Structure of Escherichia coli DNA gyrase with chirally wrapped DNA supports ratchet-and-pawl mechanism for an ATP-powered supercoiling motor
Authors: Michalczyk E / Pakosz-Stepien Z / Liston J / Gittins O / Pabis M / Heddle JG / Ghilarov D
History
DepositionJul 31, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51222.png

Downloads & links

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Map

FileDownload / File: emd_51222.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

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: 0.07
Minimum - Maximum-0.004922566 - 0.31187814
Average (Standard dev.)0.0022595152 (±0.00679641)
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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Sample components

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Entire : Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment

EntireName: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment
Components
  • Complex: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment
    • Complex: E. coli DNA gyrase
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: dsDNA
      • DNA: Mu217 DNA (159-MER)
      • DNA: Mu217 DNA (159-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment

SupramoleculeName: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: E. coli DNA gyrase

SupramoleculeName: E. coli DNA gyrase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655

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Supramolecule #3: dsDNA

SupramoleculeName: dsDNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Escherichia phage Mu (virus)

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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)
Molecular weightTheoretical: 97.646195 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTI VRMAQPFSLR YMLVDGQGNF GSIDGDSAAA MRYTEIRLAK IAHELMADLE KETVDFVDNY DGTEKIPDVM P TKIPNLLV ...String:
SSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTI VRMAQPFSLR YMLVDGQGNF GSIDGDSAAA MRYTEIRLAK IAHELMADLE KETVDFVDNY DGTEKIPDVM P TKIPNLLV NGSSGIAVGM ATNIPPHNLT EVINGCLAYI DDEDISIEGL MEHIPGPDFP TAAIINGRRG IEEAYRTGRG KV YIRARAE VEVDAKTGRE TIIVHEIPYQ VNKARLIEKI AELVKEKRVE GISALRDESD KDGMRIVIEV KRDAVGEVVL NNL YSQTQL QVSFGINMVA LHHGQPKIMN LKDIIAAFVR HRREVVTRRT IFELRKARDR AHILEALAVA LANIDPIIEL IRHA PTPAE AKTALVANPW QLGNVAAMLE RAGDDAARPE WLEPEFGVRD GLYYLTEQQA QAILDLRLQK LTGLEHEKLL DEYKE LLDQ IAELLRILGS ADRLMEVIRE ELELVREQFG DKRRTEITAN SADINLEDLI TQEDVVVTLS HQGYVKYQPL SEYEAQ RRG GKGKSAARIK EEDFIDRLLV ANTHDHILCF SSRGRVYSMK VYQLPEATRG ARGRPIVNLL PLEQDERITA ILPVTEF EE GVKVFMATAN GTVKKTVLTE FNRLRTAGKV AIKLVDGDEL IGVDLTSGED EVMLFSAEGK VVRFKESSVR AMGCNTTG V RGIRLGEGDK VVSLIVPRGD GAILTATQNG YGKRTAVAEY PTKSRATKGV ISIKVTERNG LVVGAVQVDD CDQIMMITD AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA EPVDEEDLDT IDGSAAEGDD EIAPEVDVDD EPEEELEVLF

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)
Molecular weightTheoretical: 90.891734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: Mu217 DNA (159-MER)

MacromoleculeName: Mu217 DNA (159-MER) / type: dna / ID: 3 / Number of copies: 1 / 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: Mu217 DNA (159-MER)

MacromoleculeName: Mu217 DNA (159-MER) / type: dna / ID: 4 / Number of copies: 1 / 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: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.84 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 170369
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model


PDB Unreleased entry

PDB-9gbv:
E.coli gyrase holocomplex with chirally wrapped 217 bp DNA fragment

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