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- EMDB-51222: E.coli gyrase holocomplex with chirally wrapped 217 bp DNA fragment -
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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | E.coli gyrase holocomplex with chirally wrapped 217 bp DNA fragment | ||||||||||||
![]() | composite map | ||||||||||||
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![]() | DNA gyrase / type II topoisomerase / supercoiling / DNA crossover / ISOMERASE | ||||||||||||
Function / homology | ![]() 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 | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.32 Å | ||||||||||||
![]() | Michalczyk E / Ghilarov D | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 241.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
Images | ![]() | 101.8 KB | ||
Filedesc metadata | ![]() | 7.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9gbv ![]() 51211 ![]() 51212 ![]() 51213 ![]() 51215 ![]() 51216 ![]() 51218 M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | composite map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment
Entire | Name: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment |
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Components |
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-Supramolecule #1: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment
Supramolecule | Name: 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
Supramolecule | Name: E. coli DNA gyrase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: dsDNA
Supramolecule | Name: dsDNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: DNA gyrase subunit A
Macromolecule | Name: DNA gyrase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing) |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 97.646195 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: DNA gyrase subunit B
Macromolecule | Name: DNA gyrase subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA topoisomerase (ATP-hydrolysing) |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 90.891734 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: Mu217 DNA (159-MER)
Macromolecule | Name: Mu217 DNA (159-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 65.926109 KDa |
Sequence | 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) ...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 |
-Macromolecule #4: Mu217 DNA (159-MER)
Macromolecule | Name: Mu217 DNA (159-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 66.202258 KDa |
Sequence | 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) ...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 |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.84 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 model | Type of model: NONE |
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Final reconstruction | Applied 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 assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | ![]()
PDB-9gbv: |