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- EMDB-1253: Nucleotide-dependent conformational changes in the DnaA-like core... -

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Basic information

Entry
Database: EMDB / ID: EMD-1253
TitleNucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex.
Map dataThis is a model of the ATP-gammaS bound form of the Drosophila melanogaster Origin Recognition Complex.
Sample
  • Sample: Drosophila melanogaster Origin Recognition Complex
  • Protein or peptide: ATP-bound Origin Recognition Complex
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 34.0 Å
AuthorsClarey MG
CitationJournal: Nat Struct Mol Biol / Year: 2006
Title: Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex.
Authors: Megan G Clarey / Jan P Erzberger / Patricia Grob / Andres E Leschziner / James M Berger / Eva Nogales / Michael Botchan /
Abstract: Structural details of initiator proteins for DNA replication have provided clues to the molecular events in this process. EM reconstructions of the Drosophila melanogaster origin recognition complex ...Structural details of initiator proteins for DNA replication have provided clues to the molecular events in this process. EM reconstructions of the Drosophila melanogaster origin recognition complex (ORC) reveal nucleotide-dependent conformational changes in the core of the complex. All five AAA+ domains in ORC contain a conserved structural element that, in DnaA, promotes formation of a right-handed helix, indicating that helical AAA+ substructures may be a feature of all initiators. A DnaA helical pentamer can be docked into ORC, and the location of Orc5 uniquely positions this core. The results suggest that ATP-dependent conformational changes observed in ORC derive from reorientation of the AAA+ domains. By analogy to the DNA-wrapping activity of DnaA, we posit that ORC together with Cdc6 prepares origin DNA for helicase loading through mechanisms related to the established pathway of prokaryotes.
History
DepositionJun 5, 2006-
Header (metadata) releaseAug 3, 2006-
Map releaseAug 9, 2006-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00195
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00195
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1253.gif

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Map

FileDownload / File: emd_1253.map.gz / Format: CCP4 / Size: 1.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a model of the ATP-gammaS bound form of the Drosophila melanogaster Origin Recognition Complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.18 Å/pix.
x 69 pix.
= 357.42 Å		5.18 Å/pix.
x 69 pix.
= 357.42 Å		5.18 Å/pix.
x 69 pix.
= 357.42 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.18 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00042 / Movie #1: 0.00195
Minimum - Maximum-0.00184456 - 0.00483965
Average (Standard dev.)0.0000487873 (±0.000369627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions696969
Spacing696969
CellA=B=C: 357.42 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.185.185.18
M x/y/z696969
origin x/y/z0.0000.0000.000
length x/y/z357.420357.420357.420
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS696969
D min/max/mean-0.0020.0050.000

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Supplemental data

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Sample components

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Entire : Drosophila melanogaster Origin Recognition Complex

EntireName: Drosophila melanogaster Origin Recognition Complex
Components
  • Sample: Drosophila melanogaster Origin Recognition Complex
  • Protein or peptide: ATP-bound Origin Recognition Complex

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Supramolecule #1000: Drosophila melanogaster Origin Recognition Complex

SupramoleculeName: Drosophila melanogaster Origin Recognition Complex / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 420 KDa / Theoretical: 420 KDa

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Macromolecule #1: ATP-bound Origin Recognition Complex

MacromoleculeName: ATP-bound Origin Recognition Complex / type: protein_or_peptide / ID: 1 / Oligomeric state: heterohexamer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Drosophila / Cell: Hi5 / Location in cell: Nucleus
Recombinant expressionOrganism: unidentified baculovirus

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: negative stain / Specimen holder model: OTHER

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 34.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

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