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- EMDB-3960: Cryo-EM Structure of a Licensed DNA Replication Origin -

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Basic information

Entry
Database: EMDB / ID: 3960
TitleCryo-EM Structure of a Licensed DNA Replication Origin
SampleSaccharomyces cerevisiae DNA bound unphosphorylated MCM double hexamer
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataNone
Methodsingle particle reconstruction, at 6.92 Å resolution
AuthorsAbid Ali F / Douglas ME / Locke J / Pye VE / Nans A / Diffley JFX / Costa A
CitationTo Be Published

To Be Published Search PubMed
Cryo-EM Structure of a Licensed DNA Replication Origin
Abid Ali F / Douglas ME / Locke J / Pye VE / Nans A / Diffley JFX / Costa A

Validation ReportPDB-ID: 6f0l

SummaryFull reportAbout validation report
DateDeposition: Nov 2, 2017 / Header (metadata) release: Dec 6, 2017 / Map release: Dec 6, 2017 / Last update: Dec 6, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.68
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.68
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6f0l
  • Surface level: 0.68
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_3960.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.38 Å/pix.
= 353.28 Å
256 pix
1.38 Å/pix.
= 353.28 Å
256 pix
1.38 Å/pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.38 Å
Density
Contour Level:0.68 (by author), 0.68 (movie #1):
Minimum - Maximum-0.7206352 - 2.543464
Average (Standard dev.)0.040189836 (0.17482331)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 353.28 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z353.280353.280353.280
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-0.7212.5430.040

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Supplemental data

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Sample components

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Entire Saccharomyces cerevisiae DNA bound unphosphorylated MCM double hexamer

EntireName: Saccharomyces cerevisiae DNA bound unphosphorylated MCM double hexamer
Number of components: 1
MassTheoretical: 1.2 MDa

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Component #1: protein, Saccharomyces cerevisiae DNA bound unphosphorylated MCM ...

ProteinName: Saccharomyces cerevisiae DNA bound unphosphorylated MCM double hexamer
Recombinant expression: No
MassTheoretical: 1.2 MDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Experimental details

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Sample preparation

Specimen stateparticle
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: 4.33 e/Å2 / Illumination mode: OTHER
LensImaging mode: OTHER
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: 15529
3D reconstructionSoftware: cryoSPARC / Resolution: 6.92 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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