+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3487 | |||||||||
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Title | PabMCM single octameric ring | |||||||||
Map data | PabMCM octamer | |||||||||
Sample |
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Biological species | Pyrococcus abyssi GE5 (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 22.0 Å | |||||||||
Authors | Spagnolo L / Cannone G | |||||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Structure of an octameric form of the minichromosome maintenance protein from the archaeon Pyrococcus abyssi. Authors: Giuseppe Cannone / Silvia Visentin / Adeline Palud / Ghislaine Henneke / Laura Spagnolo / Abstract: Cell division is a complex process that requires precise duplication of genetic material. Duplication is concerted by replisomes. The Minichromosome Maintenance (MCM) replicative helicase is a ...Cell division is a complex process that requires precise duplication of genetic material. Duplication is concerted by replisomes. The Minichromosome Maintenance (MCM) replicative helicase is a crucial component of replisomes. Eukaryotic and archaeal MCM proteins are highly conserved. In fact, archaeal MCMs are powerful tools for elucidating essential features of MCM function. However, while eukaryotic MCM2-7 is a heterocomplex made of different polypeptide chains, the MCM complexes of many Archaea form homohexamers from a single gene product. Moreover, some archaeal MCMs are polymorphic, and both hexameric and heptameric architectures have been reported for the same polypeptide. Here, we present the structure of the archaeal MCM helicase from Pyrococcus abyssi in its single octameric ring assembly. To our knowledge, this is the first report of a full-length octameric MCM helicase. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3487.map.gz | 175.3 KB | EMDB map data format | |
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Header (meta data) | emd-3487-v30.xml emd-3487.xml | 7.5 KB 7.5 KB | Display Display | EMDB header |
Images | emd_3487.png | 82.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3487 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3487 | HTTPS FTP |
-Validation report
Summary document | emd_3487_validation.pdf.gz | 198.8 KB | Display | EMDB validaton report |
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Full document | emd_3487_full_validation.pdf.gz | 198 KB | Display | |
Data in XML | emd_3487_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3487 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3487 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3487.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PabMCM octamer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Octameric ring composed of 8 identical subunits of PabMCM helicase
Entire | Name: Octameric ring composed of 8 identical subunits of PabMCM helicase |
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Components |
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-Supramolecule #1: Octameric ring composed of 8 identical subunits of PabMCM helicase
Supramolecule | Name: Octameric ring composed of 8 identical subunits of PabMCM helicase type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Pyrococcus abyssi GE5 (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: Modified pET28 |
Molecular weight | Theoretical: 1.26 MDa |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Staining | Type: NEGATIVE / Material: Uranyl acetate |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI 20 |
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Image recording | Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 10000 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: PROJECTION MATCHING |