EMDB-5381: Cdc6-induced Conformational Changes in ORC Bound To Or...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5381
Authors	Sun J, Kawakami H, Zech J, Speck C, Stillman B, Li H
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 1, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 1, Made by UCSF CHIMERA
Supplemental images	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)	Diagram EMDB-2081 EMDB-2080 EMDB-1928 EMDB-2078 EMDB-1438 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Structure, Vol. 20, Issue 3, Page 534-44, Year 2012
Title	Cdc6-induced conformational changes in ORC bound to origin DNA revealed by cryo-electron microscopy.
Authors	Jingchuan Sun, Hironori Kawakami, Juergen Zech, Christian Speck, Bruce Stillman, Huilin Li Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
Keywords	ABFI protein, S cerevisiae, CDC6 protein, S cerevisiae, Cell Cycle Proteins (chemistry), Cryoelectron Microscopy, DNA-Binding Proteins (chemistry), Models, Molecular, ORC1 protein, S cerevisiae, Origin Recognition Complex (chemistry), Protein Conformation, Protein Subunits (chemistry), Saccharomyces cerevisiae Proteins (chemistry), Transcription Factors (chemistry)
Links	PII: S0969-2126(12)00019-6, DOI: 10.1016/j.str.2012.01.011, PubMed: 22405012, PMC: PMC3299985

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 203.04001 A , B = 203.04001 A , C = 203.04001 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 4.23 A , Y = 4.23 A , Z = 4.23 A

CCP4 map header info

Annotation Details

cryoEM structure of Yeast Origin Recognition complex with dsDNA and Cdc6

Sample
Name	Yeast Origin Recognition Complex with dsDNA and Cdc6
Number of Components	8
Theoretical Mass	0.5 MDa
Details	ORC and Cdc6 are mixed with 66 bp DNA with ARS1 in ATPrS
Experimental Mass	0.5 MDa
Component #1: protein - ORC, Cdc6
Scientific name	Yeast Origin Recognition Complex and Cdc6
Common Name	ORC, Cdc6
Theoretical Mass	0.5 MDa
Experimental Mass	0.5 MDa
Number of Copies	1
Scientific Name of Species	Saccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of Species	ORC, Cdc6
Recombinant expression	Yes
Engineered Source	Vector: pCITE-2a Exp System: Saccharomyces cerevisiae (NCBI Taxonomy: 4932)

Experiment
Sample Preparation
Specimen Conc	0.4 mg/ml
Specimen Support Details	300 mesh lacey grid with thin continuous carbon
Specimen State	particle
Buffer	Details: 50 mM HEPES/KOH, pH 7.5, 1 mM EDTA, 1 mM EGTA, 1 mM DTT, 100 mM KGlu pH: 7.5
Vitrification
Method	Blot 5 seconds
Cryogen Name	ETHANE
Details	Vitrification instrument: FEI Vitrobot
Humidity	70
Instrument	FEI VITROBOT
Imaging
Microscope	JEOL 2010F
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	15 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 60000 X, Calibrated: 60000 X
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	3000 nm - 8000 nm
Specimen Holder
Holder	Gatan 626200 ( GATAN LIQUID NITROGEN )
Camera
Detector	Kodak so163
Image Acquisition
Scanner	NIKON COOLSCAN
Sampling Size	6.35 microns
Quant Bit Number	8

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	projection match
Software	EMAN1.8
CTF Correction	Each particle set
Resolution By Author	15
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	54000

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.4 MB .webm (WebM/VP8 format), 5.3 MB Session file for UCSF-Chimera, 26.7 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.1 MB .webm (WebM/VP8 format), 4.6 MB Session file for UCSF-Chimera, 26.7 KB