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- EMDB-56012: Negative stain-EM map of crosslinked gradient purified Sld3-Sld7-Cdc45 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-56012
TitleNegative stain-EM map of crosslinked gradient purified Sld3-Sld7-Cdc45
Map data
Sample
  • Complex: Crosslinked gradient purified Sld3-Sld7-Cdc45
KeywordsHelicase / Activation / Phosphorylation / REPLICATION
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsSaleh A / Noguchi Y / Schneider S / Aramayo R / Speck C
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust107903/Z/15/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T005378/1 United Kingdom
Cancer Research UKDRCNPG-May21/100006 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural insights into Sld3-Sld7-dependent Cdc45 loading during replication initiation
Authors: Noguchi Y / Saleh A / Schneider S / Ivanova ME / Chen ZA / Ranjha L / Aramayo R / Tognetti S / Faull SV / Rappsilber J / Speck C
History
DepositionDec 6, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56012.png

Downloads & links

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Map

FileDownload / File: emd_56012.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.92 Å/pix.
x 150 pix.
= 288. Å		1.92 Å/pix.
x 150 pix.
= 288. Å		1.92 Å/pix.
x 150 pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.53
Minimum - Maximum-0.62156194 - 3.0772228
Average (Standard dev.)0.1679849 (±0.4059508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56012_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_56012_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 : Crosslinked gradient purified Sld3-Sld7-Cdc45

EntireName: Crosslinked gradient purified Sld3-Sld7-Cdc45
Components
  • Complex: Crosslinked gradient purified Sld3-Sld7-Cdc45

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Supramolecule #1: Crosslinked gradient purified Sld3-Sld7-Cdc45

SupramoleculeName: Crosslinked gradient purified Sld3-Sld7-Cdc45 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 360 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl acetate
Details: The sample was stained with one application of 4 ul 2% (w/v) uranyl acetate solution for 1 minute before blotting.

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Electron microscopy

MicroscopeTFS TALOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 1028 / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: OTHER

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 11009
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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