EMDB-1157: ATPase-dependent cooperative binding of ORC and Cdc6 t...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1157
Authors	Speck C, Chen Z, Li H, Stillman B
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.946640809, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.946640809, Made by UCSF CHIMERA
Supplemental images	1157.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1156 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram PDB-3iyi PDB-2xyy PDB-1i84 PDB-3izg List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nat. Struct. Mol. Biol., Vol. 12, Issue 11, Page 965-71, Year 2005
Title	ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA.
Authors	Christian Speck, Zhiqiang Chen, Huilin Li, Bruce Stillman Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
Keywords	Amino Acid Sequence, CDC6 protein, S cerevisiae, Cell Cycle Proteins (metabolism), DNA (genetics, 9007-49-2), DNA Footprinting, DNA Primers, Electrophoretic Mobility Shift Assay, Microscopy, Electron, Models, Molecular, Molecular Sequence Data, Multiprotein Complexes (chemistry), Mutation (genetics), ORC1 protein, S cerevisiae, Origin Recognition Complex (metabolism), Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins (metabolism), Structure-Activity Relationship
Links	DOI: 10.1038/nsmb1002, PubMed: 16228006, PMC: PMC2952294

Map

File

EMD-1157.map ( map file in CCP4 format, 4001 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:	0.359, 0.9466408 (movie #1):
Minimum - Maximum:	0.00192997 - 5.82841
Average (Standard dev.):	0.101892 (0.462275)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	100	100	100
Origin :	0	0	0
Limit :	99	99	99
Spacing :	100	100	100

Unit Cell

A = 254 A , B = 254 A , C = 254 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 2.54 A , Y = 2.54 A , Z = 2.54 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.54	2.54	2.54
M x/y/z	100	100	100
origin x/y/z	0.000	0.000	0.000
length x/y/z	254.000	254.000	254.000
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-70	-70	-69
NX/NY/NZ	140	140	140
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	100	100	100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	0.002	5.828	0.102

Annotation Details

3D map of the yeast (Saccharomyces cerevisiae)DNA origin recognition complex (ORC) bound with initiation factor Cdc6p.

Supplement
Images
Images	1157.gif

Sample
Name	Yeast Origin Recognition complex and Cdc6p
Oligomeric State	hetero-heptamer
Number of Components	7
Experimental Mass	0.5 MDa
Theoretical Mass	0.5 MDa
Mass-estimation Method	sedimentation
Details	highly purified, monodisperse
Component #1: protein - ORC subunit 1
Scientific name	Orc1p
Common Name	ORC subunit 1
Theoretical Mass	0.120 MDa
Experimental Mass	0.12 MDa
Details	largest subunit, ATPase
Oligomeric Details	monomer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	baker's yeast
Recombinant expression	Yes
Natural Source	Organelle: Nucleus Cell Location: Nucleus Cell: yeast
Engineered Source	Vector: baculovirus bvORC1:6 Exp System: Hi-5 cell
Links	InterPro: IPR:003593, Gene Ontology: GO:0005664
Component #2: protein - ORC subunit 2
Scientific name	Orc2p
Common Name	ORC subunit 2
Theoretical Mass	0.073 MDa
Experimental Mass	0.073 MDa
Details	The second subunit
Oligomeric Details	monomer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	baker's yeast
Recombinant expression	Yes
Natural Source	Cell: yeast Cell Location: Nucleus Organelle: Nucleus
Engineered Source	Exp System: Hi-5 cell Vector: baculoviruse bvORC2:5
Links	Gene Ontology: GO:0005664, InterPro: IPR:007220
Component #3: protein - ORC subunit 3
Scientific name	Orc3p
Common Name	ORC subunit 3
Theoretical Mass	0.072 MDa
Experimental Mass	0.072 MDa
Details	The third subunit
Oligomeric Details	monomer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	baker's yeast
Recombinant expression	Yes
Natural Source	Organelle: Nucleus Cell: yeast Cell Location: Nucleus
Engineered Source	Exp System: Hi-5 cell Vector: baculoviruse bvORC3:4
Links	Gene Ontology: GO:0005664
Component #4: protein - ORC subunit 4
Scientific name	Orc4p
Common Name	ORC subunit 4
Theoretical Mass	0.061 MDa
Experimental Mass	0.061 MDa
Details	The forth subunit
Oligomeric Details	monomer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	baker's yeast
Recombinant expression	Yes
Natural Source	Cell Location: Nucleus Organelle: Nucleus Cell: yeast
Engineered Source	Exp System: Hi-5 cell Vector: baculoviruse bvORC3:4
Links	Gene Ontology: GO:0005664
Component #5: protein - ORC subunit 5
Scientific name	Orc5p
Common Name	ORC subunit 5
Theoretical Mass	0.053 MDa
Experimental Mass	0.053 MDa
Details	The fifth subunit
Oligomeric Details	monomer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	baker's yeast
Recombinant expression	Yes
Natural Source	Organelle: Nucleus Cell: yeast Cell Location: Nucleus
Engineered Source	Vector: baculoviruse bvORC2:5 Exp System: Hi-5 cell
Links	Gene Ontology: GO:0005664
Component #6: protein - ORC subunit 6
Scientific name	Orc6p
Common Name	ORC subunit 6
Theoretical Mass	0.050 MDa
Experimental Mass	0.050 MDa
Details	The sixth subunit
Oligomeric Details	monomer
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	baker's yeast
Recombinant expression	Yes
Natural Source	Organelle: Nucleus Cell: yeast Cell Location: Nucleus
Engineered Source	Vector: baculovirus bvORC1:6 Exp System: Hi-5 cell
Links	Gene Ontology: GO:0005664
Component #7: protein - Cdc6
Scientific name	Cdc6p
Common Name	Cdc6
Theoretical Mass	0.056 MDa
Experimental Mass	0.056 MDa
Details	initiation factor
Oligomeric Details	1
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	baker's yeast
Recombinant expression	Yes
Natural Source	Cell Location: Nucleus Organelle: Nucleus Cell: yeast
Engineered Source	Exp System: Escherichia coli BL21 (NCBI Taxonomy: 511693) Vector: pGex-6P1-CDC6
Links	Gene Ontology: GO:0005656

Experiment
Sample Preparation
Specimen Conc	0.02 mg/ml
Staining	Grids with adsorbed protein floated on 2% w/v uranyl acetate for 30 seconds.
Specimen Support Details	300 mesh copper grid
Specimen State	particle
Buffer	Details: 50mM HEPES-KOH, 100mM KCl, 1mM EDTA, 1mM EGTA pH: 7.5
Vitrification
Cryogen Name	ETHANE
Imaging
Microscope	OTHER
Date	2004-10-01
Electron Gun
Electron Source	LAB6
Accelerating Voltage	120 kV
Electron Dose	10 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X, Calibrated: 50000 X
Astigmatism	corrected at 250,000 X
Nominal Cs	5.6 mm
Imaging Mode	BRIGHT FIELD
Defocus	1000 nm - 2000 nm
Specimen Holder
Holder	Eucentric ( OTHER )
Tilt Angle	0 degrees - 45.0 degrees
Camera
Detector	Kodak SO163 film
Image Acquisition
Number of Digital Images	50
Sampling Size	12.7 microns
Od Range	1.5
Quant Bit Number	14
Scanner	OTHER

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	random conical tilt
Software	SPIDER, EMAN
CTF Correction	each film
Resolution By Author	20
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Class Averages	50
Number of Projections	12000
Atomic Model Fitting
Model #0
Refinement Protocol	rigid body
Details	manual fit using program O

Download

Data from EMDB

Header (meta data in XML format)

emd-1157.xml (15.5 KB)

Map data

emd_1157.map.gz (3.3 MB)

Images

1157.gif (33.4 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1157

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5.4 MB Session file for UCSF-Chimera, 20.2 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 4.9 MB Session file for UCSF-Chimera, 20.2 KB