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- EMDB-8519: Structure of Eukaryotic CMG Helicase at a Replication Fork and Im... -

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Basic information

Entry
Database: EMDB / ID: 8519
TitleStructure of Eukaryotic CMG Helicase at a Replication Fork and Implications
Map data
SampleCMG-ssDNA
  • (DNA replication licensing factor ...) x 5
  • Minichromosome maintenance protein 5
  • (DNA replication complex GINS protein ...) x 4
  • Cell division control protein 45
  • nucleic-acidNucleic acid
  • ligand
Function / homologyAAA+ ATPase domain / DNA replication licensing factor Mcm7 / MCM domain / CDC45 family / GINS complex, subunit Psf1 / DNA replication complex GINS protein Psf2 / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm5 ...AAA+ ATPase domain / DNA replication licensing factor Mcm7 / MCM domain / CDC45 family / GINS complex, subunit Psf1 / DNA replication complex GINS protein Psf2 / 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 / GINS complex subunit Sld5 / GINS complex protein Sld5, alpha-helical domain / GINS complex, subunit Psf3 / Nucleic acid-binding, OB-fold / Mini-chromosome maintenance, conserved site / GINS subunit, domain A / P-loop containing nucleoside triphosphate hydrolase / MCM N-terminal domain / Mini-chromosome maintenance protein / DNA replication complex GINS protein SLD5, C-terminal / MCM OB domain / GINS, helical bundle-like domain superfamily / MCM P-loop domain / GINS complex, subunit Psf3 superfamily / Mini-chromosome maintenance protein 2 / GINS complex protein / MCM N-terminal domain / Switching of origins to a post-replicative state / DNA replication complex GINS protein SLD5 C-terminus / MCM OB domain / MCM family signature. / Activation of the pre-replicative complex / MCM family domain profile. / CDC45-like protein / Orc1 removal from chromatin / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / MCM complex binding / negative regulation of ATP-dependent DNA helicase activity / MCM core complex / CMG complex / nuclear DNA replication / regulation of chromatin silencing at telomere / negative regulation of chromatin silencing at telomere / MCM complex / establishment of chromatin silencing / mitotic DNA replication initiation / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / regulation of DNA-dependent DNA replication initiation / nuclear pre-replicative complex / DNA replication preinitiation complex / 3'-5' DNA helicase activity / 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 / chromatin silencing at silent mating-type cassette / DNA duplex unwinding / DNA unwinding involved in DNA replication / DNA helicase activity / DNA replication origin binding / DNA replication initiation / chromatin silencing at telomere / positive regulation of G1/S transition of mitotic cell cycle / DNA helicase / helicase activity / chromosome, telomeric region / single-stranded DNA binding / DNA-dependent DNA replication / nuclear chromosome, telomeric region / cellular response to DNA damage stimulus / chromatin binding / nucleoplasm / ATP binding / metal ion binding / nucleus / 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 complex GINS protein PSF2 / DNA replication licensing factor MCM6 / DNA replication complex GINS protein SLD5 / Cell division control protein 45 / DNA replication complex GINS protein PSF3 / DNA replication complex GINS protein PSF1
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / 4.9 Å resolution
AuthorsLi B / Georgescu R / Yuan Z / Santos R / Sun J / Zhang D / Yurieva O / Li H / O'Donnell ME
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of eukaryotic CMG helicase at a replication fork and implications to replisome architecture and origin initiation.
Authors: Roxana Georgescu / Zuanning Yuan / Lin Bai / Ruda de Luna Almeida Santos / Jingchuan Sun / Dan Zhang / Olga Yurieva / Huilin Li / Michael E O'Donnell
Validation ReportPDB-ID: 5u8t

SummaryFull reportAbout validation report
DateDeposition: Dec 15, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Feb 8, 2017 / Last update: Oct 3, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5u8t
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8519.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.03 (by author), 0.03 (movie #1):
Minimum - Maximum-0.031731825 - 0.1033671
Average (Standard dev.)0.00019184175 (0.0056646327)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZYX
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 1.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0320.1030.000

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Supplemental data

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Sample components

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Entire CMG-ssDNA

EntireName: CMG-ssDNA / Number of components: 14

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Component #1: protein, CMG-ssDNA

ProteinName: CMG-ssDNA / Recombinant expression: No
MassTheoretical: 750 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Vector: pRS402

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Component #2: protein, DNA replication licensing factor MCM2

ProteinName: DNA replication licensing factor MCM2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 98.911539 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #3: protein, DNA replication licensing factor MCM3

ProteinName: DNA replication licensing factor MCM3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 107.653508 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #4: protein, DNA replication licensing factor MCM4

ProteinName: DNA replication licensing factor MCM4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.138375 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #5: protein, Minichromosome maintenance protein 5

ProteinName: Minichromosome maintenance protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.505734 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #6: protein, DNA replication licensing factor MCM6

ProteinName: DNA replication licensing factor MCM6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 113.110211 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #7: protein, DNA replication licensing factor MCM7

ProteinName: DNA replication licensing factor MCM7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 95.049875 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #8: protein, DNA replication complex GINS protein PSF1

ProteinName: DNA replication complex GINS protein PSF1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.230576 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #9: protein, DNA replication complex GINS protein PSF2

ProteinName: DNA replication complex GINS protein PSF2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.096807 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #10: protein, DNA replication complex GINS protein PSF3

ProteinName: DNA replication complex GINS protein PSF3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.977135 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #11: protein, DNA replication complex GINS protein SLD5

ProteinName: DNA replication complex GINS protein SLD5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.983617 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #12: protein, Cell division control protein 45

ProteinName: Cell division control protein 45 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 74.324836 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #13: nucleic-acid, DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*...

Nucleic-acidName: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)
MassTheoretical: 4.213742 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #14: ligand, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.506196 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
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 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 395443
3D reconstructionResolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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