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Drosophila melanogaster CMG complex bound to ADP.BeF3

by single particle reconstruction, at 28 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.42, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.42, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1832
TitleDrosophila melanogaster CMG complex bound to ADP.BeF3
MapVolume file of the ADP.BeF3-bound CMG complex
SampleDrosophila melanogaster CMG complex bound to ADP.BeF3
KeywordsAAA+ ATPase, Helicase, DNA replication
AuthorsCosta A, Ilves I, Tamberg N, Petojevic T, Nogales E, Botchan MR, Berger JM
DateDeposition: 2010-11-28, Header release: 2010-12-09, Map release: 2011-04-08, Last update: 2011-04-08
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.42, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.42, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Vol. 18, Issue 4, Page 471-7, Year 2011
TitleThe structural basis for MCM2-7 helicase activation by GINS and Cdc45.
AuthorsAlessandro Costa, Ivar Ilves, Nele Tamberg, Tatjana Petojevic, Eva Nogales, Michael R Botchan, James M Berger
Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
KeywordsAnimals, Cdc45 protein, Drosophila, Cell Cycle Proteins (metabolism), Chromosomal Proteins, Non-Histone (chemistry), Drosophila Proteins (chemistry), Enzyme Activation, MCM2 protein, Drosophila (3.6.4.12), Minichromosome Maintenance Proteins (3.6.4.12), Models, Molecular, Protein Conformation
LinksDOI: 10.1038/nsmb.2004, PubMed: 21378962, PMC: PMC4184033
Map
Fileemd_1832.map.gz ( map file in CCP4 format, 1025 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
5.7 A/pix
= 364.8 A
64 pix
5.7 A/pix
= 364.8 A
64 pix
5.7 A/pix
= 364.8 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.42 (by author), 0.42 (movie #1):
Minimum - Maximum: -0.15938 - 2.05233
Average (Standard dev.): -0.00245379 (0.155001)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-32-32
Limit313131
Spacing646464
Unit CellA= B= C: 364.8 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 5.7 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.1592.052-0.002
Annotation DetailsVolume file of the ADP.BeF3-bound CMG complex
Supplement
Images
Images
Sample
NameDrosophila melanogaster CMG complex bound to ADP.BeF3
Number of Components11
Oligomeric StateOne Mcm2-7 heterohexamer binds to one GINS heterotetramer and a Cdc45 monomer
Theoretical Mass0.7MDa
DetailsThe sample was monodisperse
Component #1: protein - Mcm2
Scientific nameMcm2
Experimental Mass0.1 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster

Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell Location: Nucleus
Cell: Baculovirus infected insect cells
Engineered SourceExpression system: Baculovirus infected insect cells
Component #2: protein - Mcm3
Scientific nameMcm3
Experimental Mass0.091 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell: Baculovirus infected insect cells
Cell Location: Nucleus
Engineered SourceExpression system: Baculovirus infected insect cells
Component #3: protein - Mcm4
Scientific nameMcm4
Experimental Mass0.097 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell: Baculovirus infected insect cells
Cell Location: Nucleus
Engineered SourceExpression system: Baculovirus infected insect cells
Component #4: protein - Mcm5
Scientific nameMcm5
Experimental Mass0.082 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell Location: Nucleus
Cell: Baculovirus infected insect cells
Engineered SourceExpression system: Baculovirus infected insect cells
Component #5: protein - Mcm6
Scientific nameMcm6
Experimental Mass0.092 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell: Baculovirus infected insect cells
Cell Location: Nucleus
Engineered SourceExpression system: Baculovirus infected insect cells
Component #6: protein - Mcm7
Scientific nameMcm7
Experimental Mass0.081 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell: Baculovirus infected insect cells
Cell Location: Nucleus
Engineered SourceExpression system: Baculovirus infected insect cells
Component #7: protein - Psf1
Scientific namePsf1
Experimental Mass0.023 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell Location: Nucleus
Cell: Baculovirus infected insect cells
Engineered SourceExpression system: Baculovirus infected insect cells
Component #8: protein - Psf2
Scientific namePsf2
Experimental Mass0.023 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell: Baculovirus infected insect cells
Cell Location: Nucleus
Engineered SourceExpression system: Baculovirus infected insect cells
Component #9: protein - Psf3
Scientific namePsf3
Experimental Mass0.025 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell Location: Nucleus
Cell: Baculovirus infected insect cells
Engineered SourceExpression system: Baculovirus infected insect cells
Component #10: protein - Sld5
Scientific nameSld5
Experimental Mass0.026 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell: Baculovirus infected insect cells
Cell Location: Nucleus
Engineered SourceExpression system: Baculovirus infected insect cells
Component #11: protein - Cdc45
Scientific nameCdc45
Experimental Mass0.066 MDa
Oligomeric DetailsMonomer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster
Common Name of SpeciesFruit Fly
NCBI taxonomy7227
Recombinant expressionYes
Natural SourceCell: Baculovirus infected insect cells
Cell Location: Nucleus
Engineered SourceExpression system: Baculovirus infected insect cells
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 30000
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderEucentric
ModelSIDE ENTRY, EUCENTRIC
Camera
DetectorGENERIC GATAN
Image Acquisition
Quant Bit Number8
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareSpider
Resolution By Author28 A
Resolution MethodFSC 0.5
Single Particle
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1832.xml (16.3 KB)
Map dataemd_1832.map.gz (348.4 KB)
Imagesemd_1832.png (135.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1832
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.4 KB