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- EMDB-56009: Cryo-EM map of MCM2-7 DH bound to DNA and two copies of Sld3-Sld7... -

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Basic information

Entry
Database: EMDB / ID: EMD-56009
TitleCryo-EM map of MCM2-7 DH bound to DNA and two copies of Sld3-Sld7 and Cdc45 (C1 symmetry)
Map data
Sample
  • Complex: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA
KeywordsHelicase / Activation / Phosphorylation / REPLICATION
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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_56009.png

Downloads & links

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Map

FileDownload / File: emd_56009.map.gz / Format: CCP4 / Size: 202.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 376 pix.
= 407.96 Å		1.09 Å/pix.
x 376 pix.
= 407.96 Å		1.09 Å/pix.
x 376 pix.
= 407.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.5094942 - 1.2406287
Average (Standard dev.)0.007290215 (±0.07819572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions376376376
Spacing376376376
CellA=B=C: 407.96002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_56009_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56009_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_56009_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 : MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

EntireName: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA
Components
  • Complex: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

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Supramolecule #1: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA

SupramoleculeName: MCM2-7 DH bound to Sld3-Sld7, Cdc45 and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 1.65 MDa

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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
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.1 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time: 30 s Blotting time: 1.5 s Blot force: +2.

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Detector mode: INTEGRATING / #0 - Number grids imaged: 1 / #0 - Number real images: 10192 / #0 - Average electron dose: 58.4 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON III (4k x 4k) / #1 - Detector mode: INTEGRATING / #1 - Number grids imaged: 1 / #1 - Number real images: 6046 / #1 - Average electron dose: 62.1 e/Å2
Electron beamAcceleration voltage: 300 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: 1.0 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

Image recording ID1
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: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 12702
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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