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ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA.

by single particle reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.946640809, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.946640809, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1157
TitleATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA.
Map3D map of the yeast (Saccharomyces cerevisiae)DNA origin recognition complex (ORC) bound with initiation factor Cdc6p.
SampleYeast Origin Recognition complex and Cdc6p
AuthorsSpeck C, Chen Z, Li H, Stillman B
DateDeposition: 2005-09-07, Header release: 2005-09-07, Map release: 2007-09-07, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.946640809, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.946640809, Image by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Vol. 12, Issue 11, Page 965-71, Year 2005
TitleATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA.
AuthorsChristian Speck, Zhiqiang Chen, Huilin Li, Bruce Stillman
Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
KeywordsAmino 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
LinksDOI: 10.1038/nsmb1002, PubMed: 16228006, PMC: PMC2952294
Map
Fileemd_1157.map.gz ( map file in CCP4 format, 3908 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
2.54 A/pix
= 254. A
100 pix
2.54 A/pix
= 254. A
100 pix
2.54 A/pix
= 254. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.359, 0.9466408 (movie #1):
Minimum - Maximum: 0.00192997 - 5.82841
Average (Standard dev.): 0.101892 (0.462275)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
Unit CellA= B= C: 254 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.54 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.542.542.54
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z254.000254.000254.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-70-70-69
NX/NY/NZ140140140
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean0.0025.8280.102
Annotation Details3D map of the yeast (Saccharomyces cerevisiae)DNA origin recognition complex (ORC) bound with initiation factor Cdc6p.
Supplement
Images
Images
Sample
NameYeast Origin Recognition complex and Cdc6p
Oligomeric Statehetero-heptamer
Number of Components7
Experimental Mass0.5MDa
Theoretical Mass0.5MDa
Mass-estimation Methodsedimentation
Detailshighly purified, monodisperse
Component #1: protein - ORC subunit 1
Scientific nameOrc1p
Common NameORC subunit 1
Theoretical Mass0.12 MDa
Experimental Mass0.12 MDa
Detailslargest subunit, ATPase
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae

Common Name of Speciesbaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceOrganelle: Nucleus
Cell Location: Nucleus
Cell: yeast
Engineered SourceVector: baculovirus bvORC1:6
Expression system: Hi-5 cell
LinksInter Pro: IPR:003593, Gene Ontology: GO:0005664
Component #2: protein - ORC subunit 2
Scientific nameOrc2p
Common NameORC subunit 2
Theoretical Mass0.073 MDa
Experimental Mass0.073 MDa
DetailsThe second subunit
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of Speciesbaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceCell: yeast
Cell Location: Nucleus
Organelle: Nucleus
Engineered SourceExpression system: Hi-5 cell
Vector: baculoviruse bvORC2:5
LinksGene Ontology: GO:0005664, Inter Pro: IPR:007220
Component #3: protein - ORC subunit 3
Scientific nameOrc3p
Common NameORC subunit 3
Theoretical Mass0.072 MDa
Experimental Mass0.072 MDa
DetailsThe third subunit
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of Speciesbaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceOrganelle: Nucleus
Cell: yeast
Cell Location: Nucleus
Engineered SourceExpression system: Hi-5 cell
Vector: baculoviruse bvORC3:4
LinksGene Ontology: GO:0005664
Component #4: protein - ORC subunit 4
Scientific nameOrc4p
Common NameORC subunit 4
Theoretical Mass0.061 MDa
Experimental Mass0.061 MDa
DetailsThe forth subunit
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of Speciesbaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceCell Location: Nucleus
Organelle: Nucleus
Cell: yeast
Engineered SourceExpression system: Hi-5 cell
Vector: baculoviruse bvORC3:4
LinksGene Ontology: GO:0005664
Component #5: protein - ORC subunit 5
Scientific nameOrc5p
Common NameORC subunit 5
Theoretical Mass0.053 MDa
Experimental Mass0.053 MDa
DetailsThe fifth subunit
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of Speciesbaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceOrganelle: Nucleus
Cell: yeast
Cell Location: Nucleus
Engineered SourceVector: baculoviruse bvORC2:5
Expression system: Hi-5 cell
LinksGene Ontology: GO:0005664
Component #6: protein - ORC subunit 6
Scientific nameOrc6p
Common NameORC subunit 6
Theoretical Mass0.05 MDa
Experimental Mass0.05 MDa
DetailsThe sixth subunit
Oligomeric Detailsmonomer
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of Speciesbaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceOrganelle: Nucleus
Cell: yeast
Cell Location: Nucleus
Engineered SourceVector: baculovirus bvORC1:6
Expression system: Hi-5 cell
LinksGene Ontology: GO:0005664
Component #7: protein - Cdc6
Scientific nameCdc6p
Common NameCdc6
Theoretical Mass0.056 MDa
Experimental Mass0.056 MDa
Detailsinitiation factor
Oligomeric Details1
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae
Common Name of Speciesbaker's yeast
NCBI taxonomy4932
Recombinant expressionYes
Natural SourceCell Location: Nucleus
Organelle: Nucleus
Cell: yeast
Engineered SourceNCBI taxonomy: 511693
Expression system: Escherichia coli BL21
Vector: pGex-6P1-CDC6
LinksGene Ontology: GO:0005656
Experiment
Sample Preparation
Specimen Conc0.02 mg/ml
StainingGrids with adsorbed protein floated on 2% w/v uranyl acetate for 30 seconds.
Specimen Support Details300 mesh copper grid
Specimen Stateparticle
BufferDetails: 50mM HEPES-KOH, 100mM KCl, 1mM EDTA, 1mM EGTA
pH: 7.5
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeJEOL 1200EX
Date2004-10-01
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 50000
Astigmatismcorrected at 250,000 X
Nominal Cs5.6 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 2000 nm
Specimen Holder
HolderEucentric
ModelOTHER
Tilt Angle0 degrees - 45.0 degrees
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
#1
#1
#1
#1
#1
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmrandom conical tilt
SoftwareSPIDER, EMAN
CTF Correctioneach film
Resolution By Author20 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages50
Number of Projections12000
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
Detailsmanual fit using program O
Download
Data from EMDB
Header (meta data in XML format)emd-1157.xml (15.6 KB)
Map dataemd_1157.map.gz (3.3 MB)
Images1157.gif (33.4 KB)
FTP directoryftp://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