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- EMDB-20744: Cryo-EM map of the S. cerevisiae primase-polymerase alpha bound t... -

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Basic information

Entry
Database: EMDB / ID: EMD-20744
TitleCryo-EM map of the S. cerevisiae primase-polymerase alpha bound to the Ctf4 trimer at 12 A resolution
Map data
Sample
  • Complex: (Ctf4)3-Pol alpha-primase
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsYuan Z / Georgescu R / Santos R / Zhang D / Bai L / Yao N / Zhao G / O'Donnell M / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research InstituteGM111472 United States
National Institutes of Health/National Human Genome Research InstituteGM45436 United States
National Institutes of Health/National Human Genome Research InstituteOD12272 United States
CitationJournal: Elife / Year: 2019
Title: Ctf4 organizes sister replisomes and Pol α into a replication factory.
Authors: Zuanning Yuan / Roxana Georgescu / Ruda de Luna Almeida Santos / Daniel Zhang / Lin Bai / Nina Y Yao / Gongpu Zhao / Michael E O'Donnell / Huilin Li /
Abstract: The current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 ...The current view is that eukaryotic replisomes are independent. Here we show that Ctf4 tightly dimerizes CMG helicase, with an extensive interface involving Psf2, Cdc45, and Sld5. Interestingly, Ctf4 binds only one Pol α-primase. Thus, Ctf4 may have evolved as a trimer to organize two helicases and one Pol α-primase into a replication factory. In the 2CMG-Ctf4-1Pol α-primase factory model, the two CMGs nearly face each other, placing the two lagging strands toward the center and two leading strands out the sides. The single Pol α-primase is centrally located and may prime both sister replisomes. The Ctf4-coupled-sister replisome model is consistent with cellular microscopy studies revealing two sister forks of an origin remain attached and are pushed forward from a protein platform. The replication factory model may facilitate parental nucleosome transfer during replication.
History
DepositionSep 20, 2019-
Header (metadata) releaseNov 6, 2019-
Map releaseNov 6, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20744.png

Downloads & links

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Map

FileDownload / File: emd_20744.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 200 pix.
= 242. Å		1.21 Å/pix.
x 200 pix.
= 242. Å		1.21 Å/pix.
x 200 pix.
= 242. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.027087493 - 0.120631956
Average (Standard dev.)0.0020914814 (±0.010094366)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 242.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.211.211.21
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z242.000242.000242.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0270.1210.002

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Supplemental data

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Sample components

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Entire : (Ctf4)3-Pol alpha-primase

EntireName: (Ctf4)3-Pol alpha-primase
Components
  • Complex: (Ctf4)3-Pol alpha-primase

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Supramolecule #1: (Ctf4)3-Pol alpha-primase

SupramoleculeName: (Ctf4)3-Pol alpha-primase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pRS

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48414
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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