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- EMDB-4164: Cryo-EM structure of the DNA bound DDK phosphorylated MCM double ... -

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Basic information

Entry
Database: EMDB / ID: 4164
TitleCryo-EM structure of the DNA bound DDK phosphorylated MCM double hexamer
Map data
SampleS. cerevisiae DNA bound DDK phosphorylated MCM double hexamer:
Function / homologyP-loop containing nucleoside triphosphate hydrolase / Mini-chromosome maintenance protein / MCM domain / MCM OB domain / AAA+ ATPase domain / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm6 ...P-loop containing nucleoside triphosphate hydrolase / Mini-chromosome maintenance protein / MCM domain / MCM OB domain / AAA+ ATPase domain / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm6 / MCM2/3/5 family / DNA replication licensing factor Mcm7 / Mini-chromosome maintenance protein 2 / MCM N-terminal domain / MCM OB domain / MCM family signature. / MCM family domain profile. / Nucleic acid-binding, OB-fold / Orc1 removal from chromatin / Mini-chromosome maintenance, conserved site / Activation of the pre-replicative complex / Switching of origins to a post-replicative state / MCM N-terminal domain / MCM complex binding / negative regulation of ATP-dependent DNA helicase activity / MCM core complex / CMG complex / nuclear DNA replication / mitotic DNA replication initiation / negative regulation of chromatin silencing at telomere / MCM complex / establishment of chromatin silencing / regulation of DNA-dependent DNA replication initiation / DNA replication preinitiation complex / nuclear pre-replicative complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / single-stranded DNA-dependent ATPase activity / double-strand break repair via break-induced replication / nuclear replication fork / DNA strand elongation involved in DNA replication / replication fork protection complex / DNA unwinding involved in DNA replication / DNA duplex unwinding / chromatin silencing at silent mating-type cassette / DNA helicase activity / DNA replication origin binding / chromatin silencing at telomere / DNA replication initiation / DNA helicase / helicase activity / chromosome, telomeric region / single-stranded DNA binding / nuclear chromosome, telomeric region / cellular response to DNA damage stimulus / chromatin binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / DNA replication licensing factor MCM6
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 7.5 Å resolution
AuthorsAbid Ali F / Douglas ME / Locke J / Pye VE / Nans A / Diffley JFX / Costa A
CitationJournal: Nat Commun / Year: 2017
Title: Cryo-EM structure of a licensed DNA replication origin.
Authors: Ferdos Abid Ali / Max E Douglas / Julia Locke / Valerie E Pye / Andrea Nans / John F X Diffley / Alessandro Costa
DateDeposition: Nov 20, 2017 / Header (metadata) release: Dec 6, 2017 / Map release: Dec 6, 2017 / Last update: Jan 24, 2018

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Structure visualization

Movie
  • Surface view colored by radius
  • Surface level: 0.645
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 0.645
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_4164.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.4 Å/pix.
= 358.4 Å
256 pix
1.4 Å/pix.
= 358.4 Å
256 pix
1.4 Å/pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour Level:0.645 (by author), 0.645 (movie #1):
Minimum - Maximum-1.2345661 - 2.771134
Average (Standard dev.)0.03267741 (0.18060562)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 358.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z358.400358.400358.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.2352.7710.033

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Supplemental data

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Sample components

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Entire S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer

EntireName: S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer
Number of components: 1
MassTheoretical: 1.2 MDa

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Component #1: protein, S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer

ProteinName: S. cerevisiae DNA bound DDK phosphorylated MCM double hexamer
Recombinant expression: No
MassTheoretical: 1.2 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 8343
3D reconstructionSoftware: cryoSPARC / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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