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Yorodumi- EMDB-1526: Single particle reconstruction of Methanothermobacter thermautotr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1526 | |||||||||
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Title | Single particle reconstruction of Methanothermobacter thermautotrophicus MCM protein bound to a 5,600bp dsDNA fragment. | |||||||||
Map data | This is an electron density map of the MthMCM helicase treated with a 5,600 bp dsDNA fragment. | |||||||||
Sample |
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Keywords | helicase / AAA+ ATPase / DNA replication | |||||||||
Biological species | synthetic construct (others) / Methanothermobacter thermautotrophicus str. Delta H (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 19.0 Å | |||||||||
Authors | Costa A / van Duinen G / Medagli B / Chong J / Sakakibara N / Kelman Z / Nair SK / Patwardhan A / Onesti S | |||||||||
Citation | Journal: EMBO J / Year: 2008 Title: Cryo-electron microscopy reveals a novel DNA-binding site on the MCM helicase. Authors: Alessandro Costa / Gijs van Duinen / Barbara Medagli / James Chong / Nozomi Sakakibara / Zvi Kelman / Satish K Nair / Ardan Patwardhan / Silvia Onesti / Abstract: The eukaryotic MCM2-7 complex is recruited at origins of replication during the G1 phase and acts as the main helicase at the replication fork during the S phase of the cell cycle. To characterize ...The eukaryotic MCM2-7 complex is recruited at origins of replication during the G1 phase and acts as the main helicase at the replication fork during the S phase of the cell cycle. To characterize the interplay between the MCM helicase and DNA prior to the melting of the double helix, we determined the structure of an archaeal MCM orthologue bound to a 5.6-kb double-stranded DNA segment, using cryo-electron microscopy. DNA wraps around the N-terminal face of a single hexameric ring. This interaction requires a conformational change within the outer belt of the MCM N-terminal domain, exposing a previously unrecognized helix-turn-helix DNA-binding motif. Our findings provide novel insights into the role of the MCM complex during the initiation step of DNA replication. | |||||||||
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_1526.map.gz | 3.1 MB | EMDB map data format | |
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Header (meta data) | emd-1526-v30.xml emd-1526.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | 1526.gif emd_1526.png emd_1526.tif | 37.9 KB 507.6 KB 286.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1526 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1526 | HTTPS FTP |
-Validation report
Summary document | emd_1526_validation.pdf.gz | 201.6 KB | Display | EMDB validaton report |
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Full document | emd_1526_full_validation.pdf.gz | 200.7 KB | Display | |
Data in XML | emd_1526_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1526 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1526 | 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_1526.map.gz / Format: CCP4 / Size: 3.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an electron density map of the MthMCM helicase treated with a 5,600 bp dsDNA fragment. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.6 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 : Methanothermobacter thermautotrophicus MCM protein bound to a 5,6...
Entire | Name: Methanothermobacter thermautotrophicus MCM protein bound to a 5,600 bp dsDNA fragment |
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Components |
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-Supramolecule #1000: Methanothermobacter thermautotrophicus MCM protein bound to a 5,6...
Supramolecule | Name: Methanothermobacter thermautotrophicus MCM protein bound to a 5,600 bp dsDNA fragment type: sample / ID: 1000 Oligomeric state: One homohexamer of MCM binds to one dsDNA fragment Number unique components: 2 |
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-Macromolecule #1: DNA
Macromolecule | Name: DNA / type: dna / ID: 1 / Name.synonym: 5,600 bp pET15b vector fragment / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #2: Mini-chromosome Maintenance complex
Macromolecule | Name: Mini-chromosome Maintenance complex / type: protein_or_peptide / ID: 2 / Name.synonym: MCM / Number of copies: 6 / Oligomeric state: Hexamer / Recombinant expression: Yes |
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Source (natural) | Organism: Methanothermobacter thermautotrophicus str. Delta H (archaea) Strain: Delta H |
Molecular weight | Theoretical: 450 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.012 mg/mL |
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Buffer | pH: 7.5 Details: 30mM Tris HCl pH 7.5, 50 mM NaCl, 5mM MgCl2, 5 mM beta-mercaptoethanol |
Grid | Details: Quantifoil R 1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4.5 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot plunger Method: Blot for 2.5 seconds at an offset of -1 before plunging |
-Electron microscopy
Microscope | FEI/PHILIPS CM200FEG |
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Image recording | Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.5 µm / Number real images: 22 / Average electron dose: 17 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder. Specimen holder model: GATAN LIQUID NITROGEN |