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

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1832
Authors	Costa A, Ilves I, Tamberg N, Petojevic T, Nogales E, Botchan MR, Berger JM
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.42, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.42, Made by UCSF CHIMERA
Supplemental images	emd_1832.png
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1833 Cite EMDB-1834 Cite EMDB-1835 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1833 PDB-4a7l PDB-4a7f EMDB-2236 PDB-4a7h List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nat. Struct. Mol. Biol., Vol. 18, Issue 4, Page 471-7, 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 Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
Keywords	Animals, Cdc45 protein, Drosophila, Cell Cycle Proteins (metabolism), Chromosomal Proteins, Non-Histone (chemistry), Drosophila Proteins (chemistry), Enzyme Activation, MCM2 protein, Drosophila, Models, Molecular, Protein Conformation
Links	DOI: 10.1038/nsmb.2004, PubMed: 21378962

Map

File

EMD-1832.map ( map file in CCP4 format, 1050 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	0.42 (by author), 0.42 (movie #1):
Minimum - Maximum:	-0.15938 - 2.05233
Average (Standard dev.):	-0.00245379 (0.155001)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	64	64	64
Origin :	-32	-32	-32
Limit :	31	31	31
Spacing :	64	64	64

Unit Cell

A = 364.8 A , B = 364.8 A , C = 364.8 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 5.7 A , Y = 5.7 A , Z = 5.7 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	5.7	5.7	5.7
M x/y/z	64	64	64
origin x/y/z	0.000	0.000	0.000
length x/y/z	364.800	364.800	364.800
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-30	-24	-70
NX/NY/NZ	61	49	141
MAP C/R/S	1	2	3
start NC/NR/NS	-32	-32	-32
NC/NR/NS	64	64	64
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-0.159	2.052	-0.002

Annotation Details

Volume file of the ADP.BeF3-bound CMG complex

Supplement
Images
Images	emd_1832.png

Sample
Name	Drosophila melanogaster CMG complex bound to ADP.BeF3
Number of Components	11
Oligomeric State	One Mcm2-7 heterohexamer binds to one GINS heterotetramer and a Cdc45 monomer
Theoretical Mass	0.7 MDa
Details	The sample was monodisperse
Component #1: protein - Mcm2
Scientific name	Mcm2
Experimental Mass	0.10 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell Location: Nucleus Cell: Baculovirus infected insect cells
Engineered Source	Exp System: Baculovirus infected insect cells
Component #2: protein - Mcm3
Scientific name	Mcm3
Experimental Mass	0.091 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell: Baculovirus infected insect cells Cell Location: Nucleus
Engineered Source	Exp System: Baculovirus infected insect cells
Component #3: protein - Mcm4
Scientific name	Mcm4
Experimental Mass	0.097 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell: Baculovirus infected insect cells Cell Location: Nucleus
Engineered Source	Exp System: Baculovirus infected insect cells
Component #4: protein - Mcm5
Scientific name	Mcm5
Experimental Mass	0.082 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell Location: Nucleus Cell: Baculovirus infected insect cells
Engineered Source	Exp System: Baculovirus infected insect cells
Component #5: protein - Mcm6
Scientific name	Mcm6
Experimental Mass	0.092 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell: Baculovirus infected insect cells Cell Location: Nucleus
Engineered Source	Exp System: Baculovirus infected insect cells
Component #6: protein - Mcm7
Scientific name	Mcm7
Experimental Mass	0.081 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell: Baculovirus infected insect cells Cell Location: Nucleus
Engineered Source	Exp System: Baculovirus infected insect cells
Component #7: protein - Psf1
Scientific name	Psf1
Experimental Mass	0.023 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell Location: Nucleus Cell: Baculovirus infected insect cells
Engineered Source	Exp System: Baculovirus infected insect cells
Component #8: protein - Psf2
Scientific name	Psf2
Experimental Mass	0.023 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell: Baculovirus infected insect cells Cell Location: Nucleus
Engineered Source	Exp System: Baculovirus infected insect cells
Component #9: protein - Psf3
Scientific name	Psf3
Experimental Mass	0.025 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell Location: Nucleus Cell: Baculovirus infected insect cells
Engineered Source	Exp System: Baculovirus infected insect cells
Component #10: protein - Sld5
Scientific name	Sld5
Experimental Mass	0.026 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell: Baculovirus infected insect cells Cell Location: Nucleus
Engineered Source	Exp System: Baculovirus infected insect cells
Component #11: protein - Cdc45
Scientific name	Cdc45
Experimental Mass	0.066 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Drosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Species	Fruit Fly
Recombinant expression	Yes
Natural Source	Cell: Baculovirus infected insect cells Cell Location: Nucleus
Engineered Source	Exp System: Baculovirus infected insect cells

Experiment
Sample Preparation
Specimen State	particle
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	FEI TECNAI 12
Electron Gun
Electron Source	LAB6
Accelerating Voltage	120 kV
Electron Dose	20 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 30000 X,
Imaging Mode	BRIGHT FIELD
Specimen Holder
Holder	Eucentric ( SIDE ENTRY, EUCENTRIC )
Camera
Detector	GATAN CCD
Image Acquisition
Quant Bit Number	8

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Projection matching
Software	Spider
Resolution By Author	28
Resolution Method	FSC at 0.5 cut-off

Download

Data from EMDB

Header (meta data in XML format)

emd-1832.xml (16.3 KB)

Map data

emd_1832.map.gz (348.4 KB)

Images

emd_1832.png (135.1 KB)

FTP directory

ftp://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