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- EMDB-1832: Drosophila melanogaster CMG complex bound to ADP.BeF3 -

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Basic information

Entry
Database: EMDB / ID: EMD-1832
TitleDrosophila melanogaster CMG complex bound to ADP.BeF3
Map dataVolume file of the ADP.BeF3-bound CMG complex
Sample
  • Sample: Drosophila melanogaster CMG complex bound to ADP.BeF3
  • Protein or peptide: x 11 types
KeywordsAAA+ ATPase / Helicase / DNA replication
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / Resolution: 28.0 Å
AuthorsCosta A / Ilves I / Tamberg N / Petojevic T / Nogales E / Botchan MR / Berger JM
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: The structural basis for MCM2-7 helicase activation by GINS and Cdc45.
Authors: Alessandro Costa / Ivar Ilves / Nele Tamberg / Tatjana Petojevic / Eva Nogales / Michael R Botchan / James M Berger /
Abstract: Two central steps for initiating eukaryotic DNA replication involve loading of the Mcm2-7 helicase onto double-stranded DNA and its activation by GINS-Cdc45. To better understand these events, we ...Two central steps for initiating eukaryotic DNA replication involve loading of the Mcm2-7 helicase onto double-stranded DNA and its activation by GINS-Cdc45. To better understand these events, we determined the structures of Mcm2-7 and the CMG complex by using single-particle electron microscopy. Mcm2-7 adopts two conformations--a lock-washer-shaped spiral state and a planar, gapped-ring form--in which Mcm2 and Mcm5 flank a breach in the helicase perimeter. GINS and Cdc45 bridge this gap, forming a topologically closed assembly with a large interior channel; nucleotide binding further seals off the discontinuity between Mcm2 and Mcm5, partitioning the channel into two smaller pores. Together, our data help explain how GINS and Cdc45 activate Mcm2-7, indicate that Mcm2-7 loading may be assisted by a natural predisposition of the hexamer to form open rings, and suggest a mechanism by which the CMG complex assists DNA strand separation.
History
DepositionNov 28, 2010-
Header (metadata) releaseDec 9, 2010-
Map releaseApr 8, 2011-
UpdateApr 8, 2011-
Current statusApr 8, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.42
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.42
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1832.png

Downloads & links

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Map

FileDownload / File: emd_1832.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume file of the ADP.BeF3-bound CMG complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.7 Å/pix.
x 64 pix.
= 364.8 Å		5.7 Å/pix.
x 64 pix.
= 364.8 Å		5.7 Å/pix.
x 64 pix.
= 364.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.42 / Movie #1: 0.42
Minimum - Maximum-0.15938 - 2.05233
Average (Standard dev.)-0.00245379 (±0.155001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 364.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.75.75.7
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z364.800364.800364.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-0.1592.052-0.002

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Supplemental data

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Sample components

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Entire : Drosophila melanogaster CMG complex bound to ADP.BeF3

EntireName: Drosophila melanogaster CMG complex bound to ADP.BeF3
Components
  • Sample: Drosophila melanogaster CMG complex bound to ADP.BeF3
  • Protein or peptide: Mcm2
  • Protein or peptide: Mcm3
  • Protein or peptide: Mcm4
  • Protein or peptide: Mcm5
  • Protein or peptide: Mcm6
  • Protein or peptide: Mcm7
  • Protein or peptide: Psf1
  • Protein or peptide: Psf2
  • Protein or peptide: Psf3
  • Protein or peptide: Sld5
  • Protein or peptide: Cdc45

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Supramolecule #1000: Drosophila melanogaster CMG complex bound to ADP.BeF3

SupramoleculeName: Drosophila melanogaster CMG complex bound to ADP.BeF3 / type: sample / ID: 1000 / Details: The sample was monodisperse
Oligomeric state: One Mcm2-7 heterohexamer binds to one GINS heterotetramer and a Cdc45 monomer
Number unique components: 11
Molecular weightTheoretical: 700 KDa

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Macromolecule #1: Mcm2

MacromoleculeName: Mcm2 / type: protein_or_peptide / ID: 1 / Name.synonym: Mcm2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 100 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #2: Mcm3

MacromoleculeName: Mcm3 / type: protein_or_peptide / ID: 2 / Name.synonym: Mcm3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 91 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #3: Mcm4

MacromoleculeName: Mcm4 / type: protein_or_peptide / ID: 3 / Name.synonym: Mcm4 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 97 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #4: Mcm5

MacromoleculeName: Mcm5 / type: protein_or_peptide / ID: 4 / Name.synonym: Mcm5 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 82 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #5: Mcm6

MacromoleculeName: Mcm6 / type: protein_or_peptide / ID: 5 / Name.synonym: Mcm6 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 92 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #6: Mcm7

MacromoleculeName: Mcm7 / type: protein_or_peptide / ID: 6 / Name.synonym: Mcm7 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 81 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #7: Psf1

MacromoleculeName: Psf1 / type: protein_or_peptide / ID: 7 / Name.synonym: Psf1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 23 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #8: Psf2

MacromoleculeName: Psf2 / type: protein_or_peptide / ID: 8 / Name.synonym: Psf2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 23 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #9: Psf3

MacromoleculeName: Psf3 / type: protein_or_peptide / ID: 9 / Name.synonym: Psf3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 25 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #10: Sld5

MacromoleculeName: Sld5 / type: protein_or_peptide / ID: 10 / Name.synonym: Sld5 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 26 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Macromolecule #11: Cdc45

MacromoleculeName: Cdc45 / type: protein_or_peptide / ID: 11 / Name.synonym: Cdc45 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 66 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Average electron dose: 20 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 30000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider

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