[English] 日本語
Yorodumi
- EMDB-1157: ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA. -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1157
TitleATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA.
SampleYeast Origin Recognition complex and Cdc6p
SourceSaccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
Map data3D map of the yeast (Saccharomyces cerevisiae)DNA origin recognition complex (ORC) bound with initiation factor Cdc6p.
Methodsingle particle reconstruction, at 20 A resolution
AuthorsSpeck C / Chen Z / Li H / Stillman B
CitationNat. Struct. Mol. Biol., 2005, 12, 965-971

Nat. Struct. Mol. Biol., 2005, 12, 965-971 StrPapers
ATPase-dependent cooperative binding of ORC and Cdc6 to origin DNA.
Christian Speck / Zhiqiang Chen / Huilin Li / Bruce Stillman

DateDeposition: Sep 7, 2005 / Header (metadata) release: Sep 7, 2005 / Map release: Sep 7, 2007 / Last update: Sep 7, 2005

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.946640809
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.946640809
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_1157.map.gz (map file in CCP4 format, 3908 KB)
Projections & slices
Size
Brightness
Contrast
Others
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.

Voxel sizeX=Y=Z: 2.54 A
Density
Contour Level:0.359, 0.9466408 (movie #1):
Minimum - Maximum0.00192997 - 5.82841
Average (Standard dev.)0.101892 (0.462275)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
CellA=B=C: 254 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean0.0025.8280.102

-
Supplemental data

-
Sample components

+
Entire Yeast Origin Recognition complex and Cdc6p

EntireName: Yeast Origin Recognition complex and Cdc6p / Details: highly purified, monodisperse / Oligomeric State: hetero-heptamer / Number of components: 7
MassTheoretical: 500 kDa / Experimental: 500 kDa / Measured by: sedimentation

+
Component #1: protein, Orc1p

ProteinName: Orc1p / a.k.a: ORC subunit 1 / Oligomeric Details: monomer / Details: largest subunit, ATPase / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 120 kDa / Experimental: 120 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Hi-5 cell / Vector: baculovirus bvORC1:6
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
External referencesInterPro: InterPro: 003593 / Gene Ontology: GO: 0005664

+
Component #2: protein, Orc2p

ProteinName: Orc2p / a.k.a: ORC subunit 2 / Oligomeric Details: monomer / Details: The second subunit / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 73 kDa / Experimental: 73 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Hi-5 cell / Vector: baculoviruse bvORC2:5
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
External referencesGene Ontology: GO: 0005664 / InterPro: InterPro: 007220

+
Component #3: protein, Orc3p

ProteinName: Orc3p / a.k.a: ORC subunit 3 / Oligomeric Details: monomer / Details: The third subunit / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 72 kDa / Experimental: 72 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Hi-5 cell / Vector: baculoviruse bvORC3:4
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
External referencesGene Ontology: GO: 0005664

+
Component #4: protein, Orc4p

ProteinName: Orc4p / a.k.a: ORC subunit 4 / Oligomeric Details: monomer / Details: The forth subunit / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 61 kDa / Experimental: 61 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Hi-5 cell / Vector: baculoviruse bvORC3:4
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
External referencesGene Ontology: GO: 0005664

+
Component #5: protein, Orc5p

ProteinName: Orc5p / a.k.a: ORC subunit 5 / Oligomeric Details: monomer / Details: The fifth subunit / Number of Copies: 1 / Recombinant expression: Yes
MassTheoretical: 53 kDa / Experimental: 53 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Hi-5 cell / Vector: baculoviruse bvORC2:5
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
External referencesGene Ontology: GO: 0005664

+
Component #6: protein, Orc6p

ProteinName: Orc6p / a.k.a: ORC subunit 6 / Oligomeric Details: monomer / Details: The sixth subunit / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 50 kDa / Experimental: 50 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Hi-5 cell / Vector: baculovirus bvORC1:6
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
External referencesGene Ontology: GO: 0005664

+
Component #7: protein, Cdc6p

ProteinName: Cdc6p / a.k.a: Cdc6 / Oligomeric Details: 1 / Details: initiation factor / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 56 kDa / Experimental: 56 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / baker's yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli bl21 / bacteria / image: Escherichia coli
Vector: pGex-6P1-CDC6
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: yeast
External referencesGene Ontology: GO: 0005656

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.02 mg/ml
Buffer solution: 50mM HEPES-KOH, 100mM KCl, 1mM EDTA, 1mM EGTA
pH: 7.5
Support film300 mesh copper grid
StainingGrids with adsorbed protein floated on 2% w/v uranyl acetate for 30 seconds.
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

ImagingMicroscope: JEOL 1200EX / Date: Oct 1, 2004
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: corrected at 250,000 X / Cs: 5.6 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm
Specimen HolderHolder: Eucentric / Model: OTHER / Tilt Angle: 0 - 45.0 deg.
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisition
50
Image acquisition
127
Image acquisition
15
Image acquisition
14
Image acquisition
OTHER

-
Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 50 / Number of projections: 12000 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: random conical tilt / Software: SPIDER, EMAN / CTF correction: each film / Resolution: 20 A / Resolution method: FSC 0.5

-
Atomic model buiding

Modeling #1Refinement protocol: rigid body / Details: manual fit using program O

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more