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- EMDB-18603: E. coli DNA gyrase bound to a linear part of a DNA minicircle -

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Basic information

Entry
Database: EMDB / ID: EMD-18603
TitleE. coli DNA gyrase bound to a linear part of a DNA minicircle
Map data
Sample
  • Complex: E. coli DNA gyrase in complex with dsDNA minicircles
    • Complex: E. coli DNA gyrase
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: dsDNA minicircles
      • DNA: DNA (30-MER)
      • DNA: DNA (30-MER)
KeywordsDNA-protein complex / type IIA topoisomerase DNA gyrase / 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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsVayssieres M / Lamour V / Marechal N
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Science / Year: 2024
Title: Structural basis of DNA crossover capture by DNA gyrase.
Authors: Marlène Vayssières / Nils Marechal / Long Yun / Brian Lopez Duran / Naveen Kumar Murugasamy / Jonathan M Fogg / Lynn Zechiedrich / Marc Nadal / Valérie Lamour /
Abstract: DNA supercoiling must be precisely regulated by topoisomerases to prevent DNA entanglement. The interaction of type IIA DNA topoisomerases with two DNA molecules, enabling the transport of one duplex ...DNA supercoiling must be precisely regulated by topoisomerases to prevent DNA entanglement. The interaction of type IIA DNA topoisomerases with two DNA molecules, enabling the transport of one duplex through the transient double-stranded break of the other, remains elusive owing to structures derived solely from single linear duplex DNAs lacking topological constraints. Using cryo-electron microscopy, we solved the structure of DNA gyrase bound to a negatively supercoiled minicircle DNA. We show how DNA gyrase captures a DNA crossover, revealing both conserved molecular grooves that accommodate the DNA helices. Together with molecular tweezer experiments, the structure shows that the DNA crossover is of positive chirality, reconciling the binding step of gyrase-mediated DNA relaxation and supercoiling in a single structure.
History
DepositionOct 6, 2023-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18603.png

Downloads & links

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Map

FileDownload / File: emd_18603.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.
= 331.008 Å		0.86 Å/pix.
x 384 pix.
= 331.008 Å		0.86 Å/pix.
x 384 pix.
= 331.008 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-4.43992 - 9.474264
Average (Standard dev.)0.006539218 (±0.18562143)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 331.008 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18603_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_18603_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 : E. coli DNA gyrase in complex with dsDNA minicircles

EntireName: E. coli DNA gyrase in complex with dsDNA minicircles
Components
  • Complex: E. coli DNA gyrase in complex with dsDNA minicircles
    • Complex: E. coli DNA gyrase
      • Protein or peptide: DNA gyrase subunit A
      • Protein or peptide: DNA gyrase subunit B
    • Complex: dsDNA minicircles
      • DNA: DNA (30-MER)
      • DNA: DNA (30-MER)

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Supramolecule #1: E. coli DNA gyrase in complex with dsDNA minicircles

SupramoleculeName: E. coli DNA gyrase in complex with dsDNA minicircles / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 745 KDa

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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)

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Supramolecule #3: dsDNA minicircles

SupramoleculeName: dsDNA minicircles / 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
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 97.072578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTI VRMAQPFSLR YMLVDGQGNF GSIDGDSAAA MRFTEIRLAK IAHELMADLE KETVDFVDNY DGTEKIPDVM P TKIPNLLV ...String:
MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN KAYKKSARVV GDVIGKYHPH GDSAVYDTI VRMAQPFSLR YMLVDGQGNF GSIDGDSAAA MRFTEIRLAK 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 EPEEE

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: 90.073922 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEII VTIHADNSVS VQDDGRGIPT GIHPEEGVS AAEVIMTVLH AGGKFDDNSY KVSGGLHGVG VSVVNALSQK LELVIQREGK IHRQIYEHGV PQAPLAVTGE T EKTGTMVR ...String:
MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEII VTIHADNSVS VQDDGRGIPT GIHPEEGVS AAEVIMTVLH AGGKFDDNSY KVSGGLHGVG VSVVNALSQK LELVIQREGK IHRQIYEHGV PQAPLAVTGE T EKTGTMVR FWPSLETFTN VTEFEYEILA KRLRELSFLN SGVSIRLRDK RDGKEDHFHY EGGIKAFVEY LNKNKTPIHP NI FYFSTEK DGIGVEVALQ WNDGFQENIY CFTNNIPQRD GGTHLAGFRA AMTRTLNAYM DKEGYSKKAK VSATGDDARE GLI AVVSVK VPDPKFSSQT KDKLVSSEVK SAVEQQMNEL LAEYLLENPT DAKIVVGKII DAARAREAAR RAREMTRRKG ALDL AGLPG KLADCQERDP ALSELYLVEG DSAGGSAKQG RNRKNQAILP LKGKILNVEK ARFDKMLSSQ EVATLITALG CGIGR DEYN PDKLRYHSII IMTDADVDGS HIRTLLLTFF YRQMPEIVER GHVYIAQPPL YKVKKGKQEQ YIKDDEAMDQ YQISIA LDG ATLHTNASAP ALAGEALEKL VSEYNATQKM INRMERRYPK AMLKELIYQP TLTEADLSDE QTVTRWVNAL VSELNDK EQ HGSQWKFDVH TNAEQNLFEP IVRVRTHGVD TDYPLDHEFI TGGEYRRICT LGEKLRGLLE EDAFIERGER RQPVASFE Q ALDWLVKESR RGLSIQRYKG LGEMNPEQLW ETTMDPESRR MLRVTVKDAI AADQLFTTLM GDAVEPRRAF IEENALKAA NIDI

UniProtKB: DNA gyrase subunit B

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Macromolecule #3: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.080827 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)

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Macromolecule #4: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.351247 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Average electron dose: 46.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 81000
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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V3.3.2) / Number images used: 101436
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6rkw


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-8qqs:
E. coli DNA gyrase bound to a linear part of a DNA minicircle

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