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- EMDB-1253: Nucleotide-dependent conformational changes in the DnaA-like core... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-1253 | |||||||||
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Title | Nucleotide-dependent conformational changes in the DnaA-like core of the origin recognition complex. | |||||||||
![]() | This is a model of the ATP-gammaS bound form of the Drosophila melanogaster Origin Recognition Complex. | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 34.0 Å | |||||||||
![]() | Clarey MG | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 6.7 KB 6.7 KB | Display Display | ![]() |
Images | ![]() | 20.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 212.6 KB | Display | ![]() |
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Full document | ![]() | 211.7 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a model of the ATP-gammaS bound form of the Drosophila melanogaster Origin Recognition Complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.18 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Drosophila melanogaster Origin Recognition Complex
Entire | Name: Drosophila melanogaster Origin Recognition Complex |
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Components |
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-Supramolecule #1000: Drosophila melanogaster Origin Recognition Complex
Supramolecule | Name: Drosophila melanogaster Origin Recognition Complex / type: sample / ID: 1000 / Number unique components: 1 |
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Molecular weight | Experimental: 420 KDa / Theoretical: 420 KDa |
-Macromolecule #1: ATP-bound Origin Recognition Complex
Macromolecule | Name: ATP-bound Origin Recognition Complex / type: protein_or_peptide / ID: 1 / Oligomeric state: heterohexamer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI 12 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: negative stain / Specimen holder model: OTHER |
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Image processing
Final reconstruction | Applied 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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