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- EMDB-13663: CryoEM structure of DnaD dimer from Bacillus subtilis -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-13663
TitleCryoEM structure of DnaD dimer from Bacillus subtilis
Map dataStructure of the dimeric state of DnaD
Sample
  • Complex: Dimer of the replication initiation protein DnaD
KeywordsReplication / Initiation / Bacteria / Bacillus subtilis / DNA BINDING PROTEIN
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.1 Å
AuthorsWinterhalter C / Pelliciari S / Cronin N / Costa TRD / Ilangovan I / Murray H
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust204985/Z/16/Z United Kingdom
CitationJournal: Biorxiv / Year: 2022
Title: The DNA replication initiation protein DnaD is recruited to a specific strand of the Bacillus subtilis chromosome origin
Authors: Winterhalter C / Pelliciari S / Stevens D / Fenyk S / Marchand E / Cronin NB / Soultanas P / Costa TRD / Ilangovan A / Murray H
History
DepositionOct 1, 2021-
Header (metadata) releaseOct 12, 2022-
Map releaseOct 12, 2022-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_13663.png

Downloads & links

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Map

FileDownload / File: emd_13663.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the dimeric state of DnaD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 360 pix.
= 241.2 Å		0.67 Å/pix.
x 360 pix.
= 241.2 Å		0.67 Å/pix.
x 360 pix.
= 241.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.21003602 - 0.4032008
Average (Standard dev.)-0.00018825076 (±0.014531805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 241.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Dimer of the replication initiation protein DnaD

EntireName: Dimer of the replication initiation protein DnaD
Components
  • Complex: Dimer of the replication initiation protein DnaD

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Supramolecule #1: Dimer of the replication initiation protein DnaD

SupramoleculeName: Dimer of the replication initiation protein DnaD / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 54 KDa

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.1 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 73190
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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