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- EMDB-51213: Gyrase holocomplex with chirally wrapped DNA: a focussed map for ... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-51213
TitleGyrase holocomplex with chirally wrapped DNA: a focussed map for the CTD II & T-DNA
Map data
Sample
  • Complex: Ternary complex of E.coli DNA gyrase with 217 bp linear dsDNA fragment
KeywordsDNA gyrase / type II topoisomerase / supercoiling / DNA crossover / ISOMERASE
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 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 30, 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_51213.png

Downloads & links

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Map

FileDownload / File: emd_51213.map.gz / Format: CCP4 / Size: 512 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 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: 0.085
Minimum - Maximum-0.083983 - 0.23343867
Average (Standard dev.)-0.0000022587228 (±0.004963431)
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: #1

Fileemd_51213_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51213_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

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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, #3-#5
Source (natural)Organism: Escherichia coli (E. coli) / Strain: MG1655

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 53570
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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