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- EMDB-51218: E.coli gyrase holocomplex with 217 bp chirally wrapped DNA (conse... -

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Basic information

Entry
Database: EMDB / ID: EMD-51218
TitleE.coli gyrase holocomplex with 217 bp chirally wrapped DNA (consensus map)
Map dataConsensus map
Sample
  • Complex: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment
    • Protein or peptide: DNA gyrase subunit A
    • Protein or peptide: DNA gyrase subunit B
    • DNA: Mu217 DNA fragment
    • DNA: Mu217 DNA fragment
KeywordsDNA gyrase / type II topoisomerase / supercoiling / 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) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling 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) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling 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 / 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 / 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 / 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: 2.3 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) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51218.png

Downloads & links

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Map

FileDownload / File: emd_51218.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus 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: 0.05
Minimum - Maximum-0.112217166 - 0.4625476
Average (Standard dev.)0.000013008056 (±0.006222079)
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_51218_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51218_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 : 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
    • Protein or peptide: DNA gyrase subunit A
    • Protein or peptide: DNA gyrase subunit B
    • DNA: Mu217 DNA fragment
    • DNA: Mu217 DNA fragment

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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: all
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655

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Macromolecule #1: DNA gyrase subunit A

MacromoleculeName: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Details: Gyrase subunit A / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY MLVDGQGNFG SIDGDSAAAM RYTEIRLAKI AHELMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG ...String:
SSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY MLVDGQGNFG SIDGDSAAAM RYTEIRLAKI AHELMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT NIPPHNLTEV INGCLAYIDD EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV YIRARAEVEV DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKEKRVEGIS ALRDESDKDG MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI IAAFVRHRRE VVTRRTIFEL RKARDRAHIL EALAVALANI DPIIELIRHA PTPAEAKTAL VANPWQLGNV AAMLERAGDD AARPEWLEPE FGVRDGLYYL TEQQAQAILD LRLQKLTGLE HEKLLDEYKE LLDQIAELLR ILGSADRLME VIREELELVR EQFGDKRRTE ITANSADINL EDLITQEDVV VTLSHQGYVK YQPLSEYEAQ RRGGKGKSAA RIKEEDFIDR LLVANTHDHI LCFSSRGRVY SMKVYQLPEA TRGARGRPIV NLLPLEQDER ITAILPVTEF EEGVKVFMAT ANGTVKKTVL TEFNRLRTAG KVAIKLVDGD ELIGVDLTSG EDEVMLFSAE GKVVRFKESS VRAMGCNTTG VRGIRLGEGD KVVSLIVPRG DGAILTATQN GYGKRTAVAE YPTKSRATKG VISIKVTERN GLVVGAVQVD DCDQIMMITD AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA EPVDEEDLDT IDGSAAEGDD EIAPEVDVDD EPEEELEVLF Q

UniProtKB: DNA gyrase subunit A

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Macromolecule #3: DNA gyrase subunit B

MacromoleculeName: DNA gyrase subunit B / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPSNSYDSSS IKVLKGLDAV RKRPGMYIGD TDDGTGLHHM VFEVVDNAID EALAGHCKEI IVTIHADNSV SVQDDGRGIP TGIHPEEGVS AAEVIMTVLH AGGKFDDNSY KVSGGLHGVG VSVVNALSQK LELVIQREGK IHRQIYEHGV PQAPLAVTGE TEKTGTMVRF ...String:
GPSNSYDSSS IKVLKGLDAV RKRPGMYIGD TDDGTGLHHM VFEVVDNAID EALAGHCKEI IVTIHADNSV SVQDDGRGIP TGIHPEEGVS AAEVIMTVLH AGGKFDDNSY KVSGGLHGVG VSVVNALSQK LELVIQREGK IHRQIYEHGV PQAPLAVTGE TEKTGTMVRF WPSLETFTNV TEFEYEILAK RLRELSFLNS GVSIRLRDKR DGKEDHFHYE GGIKAFVEYL NKNKTPIHPN IFYFSTEKDG IGVEVALQWN DGFQENIYCF TNNIPQRDGG THLAGFRAAM TRTLNAYMDK EGYSKKAKVS ATGDDAREGL IAVVSVKVPD PKFSSQTKDK LVSSEVKSAV EQQMNELLAE YLLENPTDAK IVVGKIIDAA RAREAARRAR EMTRRKGALD LAGLPGKLAD CQERDPALSE LYLVEGDSAG GSAKQGRNRK NQAILPLKGK ILNVEKARFD KMLSSQEVAT LITALGCGIG RDEYNPDKLR YHSIIIMTDA DVDGSHIRTL LLTFFYRQMP EIVERGHVYI AQPPLYKVKK GKQEQYIKDD EAMDQYQISI ALDGATLHTN ASAPALAGEA LEKLVSEYNA TQKMINRMER RYPKAMLKEL IYQPTLTEAD LSDEQTVTRW VNALVSELND KEQHGSQWKF DVHTNAEQNL FEPIVRVRTH GVDTDYPLDH EFITGGEYRR ICTLGEKLRG LLEEDAFIER GERRQPVASF EQALDWLVKE SRRGLSIQRY KGLGEMNPEQ LWETTMDPES RRMLRVTVKD AIAADQLFTT LMGDAVEPRR AFIEENALKA ANIDIENLYF Q

UniProtKB: DNA gyrase subunit B

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Macromolecule #4: Mu217 DNA fragment

MacromoleculeName: Mu217 DNA fragment / type: dna / ID: 4 / Classification: DNA
Source (natural)Organism: Escherichia phage Mu (virus)
SequenceString: ACTGGAGAAA GAAAGTGAAA GGAAGATAAA ACGGGATTCA TACACCGTTA AATACCGGTT TAAAAATCCC GTGGCGCGTT TTAAAAAATC TGTGCGGGTG ATTTTATGCC TGATTCTGTT TATTGCCTCA GAGCGGCGCT GACGCGTTTT CTGATGGCAT CAAAAATTTC ...String:
ACTGGAGAAA GAAAGTGAAA GGAAGATAAA ACGGGATTCA TACACCGTTA AATACCGGTT TAAAAATCCC GTGGCGCGTT TTAAAAAATC TGTGCGGGTG ATTTTATGCC TGATTCTGTT TATTGCCTCA GAGCGGCGCT GACGCGTTTT CTGATGGCAT CAAAAATTTC CTGTTCCCCG GTCTTATCCA GCCCCATATA AGGACGCGCA GGAA

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Macromolecule #5: Mu217 DNA fragment

MacromoleculeName: Mu217 DNA fragment / type: dna / ID: 5 / Classification: DNA
Source (natural)Organism: Escherichia phage Mu (virus)
SequenceString: TTCCTGCGCG TCCTTATATG GGGCTGGATA AGACCGGGGA ACAGGAAATT TTTGATGCCA TCAGAAAACG CGTCAGCGCC GCTCTGAGGC AATAAACAGA ATCAGGCATA AAATCACCCG CACAGATTTT TTAAAACGCG CCACGGGATT TTTAAACCGG TATTTAACGG ...String:
TTCCTGCGCG TCCTTATATG GGGCTGGATA AGACCGGGGA ACAGGAAATT TTTGATGCCA TCAGAAAACG CGTCAGCGCC GCTCTGAGGC AATAAACAGA ATCAGGCATA AAATCACCCG CACAGATTTT TTAAAACGCG CCACGGGATT TTTAAACCGG TATTTAACGG TGTATGAATC CCGTTTTATC TTCCTTTCAC TTTCTTTCTC CAGT

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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
GridModel: Quantifoil R2/1 / Material: COPPER
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: 2.3 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
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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