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Yorodumi- EMDB-6292: An EM structure of the helicase-loader complex in G. kaustophilus... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6292 | |||||||||
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Title | An EM structure of the helicase-loader complex in G. kaustophilus suggesting an early stage conformation in Gram-positive bacteria | |||||||||
Map data | Reconstruction of the GkDnaC-GkDnaI helicase-loader complex in a putative early stage conformation | |||||||||
Sample |
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Keywords | DNA replication / primosome assembly / helicase-loader complex | |||||||||
Biological species | Geobacillus kaustophilus (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 19.0 Å | |||||||||
Authors | Lin Y-C / Vankadari N / Hsiao C-D | |||||||||
Citation | Journal: To Be Published Title: An EM structure of the helicase-loader complex in G. kaustophilus suggesting an early stage conformation Authors: Lin Y-C / Vankadari N / Hsiao C-D | |||||||||
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_6292.map.gz | 5 MB | EMDB map data format | |
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Header (meta data) | emd-6292-v30.xml emd-6292.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_6292.png | 52.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6292 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6292 | HTTPS FTP |
-Validation report
Summary document | emd_6292_validation.pdf.gz | 78.5 KB | Display | EMDB validaton report |
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Full document | emd_6292_full_validation.pdf.gz | 77.6 KB | Display | |
Data in XML | emd_6292_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6292 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6292 | 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_6292.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the GkDnaC-GkDnaI helicase-loader complex in a putative early stage conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.75 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 : GkDnaC-GkDnaI helicase-loader complex
Entire | Name: GkDnaC-GkDnaI helicase-loader complex |
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Components |
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-Supramolecule #1000: GkDnaC-GkDnaI helicase-loader complex
Supramolecule | Name: GkDnaC-GkDnaI helicase-loader complex / type: sample / ID: 1000 Oligomeric state: One homohexamer of GkDnaC binds to one dimer (or two monomers) of GkDnaI Number unique components: 2 |
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Molecular weight | Theoretical: 378 KDa |
-Macromolecule #1: GkDnaC-GkDnaI complex
Macromolecule | Name: GkDnaC-GkDnaI complex / type: protein_or_peptide / ID: 1 Oligomeric state: one GkDnaC hexamer + two GkDnaI monomer (or one GkDnaI dimer) Recombinant expression: Yes |
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Source (natural) | Organism: Geobacillus kaustophilus (bacteria) / Strain: HTA426 |
Molecular weight | Theoretical: 378 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21DE3 |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.02 mg/mL |
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Buffer | pH: 8.5 Details: 20 mM Tris-HCl pH 8.5, 200 mM NaCl, 5mM MgCl2, 1 mM beta-mercaptoethanol, 1 mM ATP-gamma-S |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein floated sequentially on three drops of 0.75 % w/v uranyl formate each for 20 seconds and then left for staining for 1 minute. |
Grid | Details: 300 mesh Cu grid with thin carbon support, glow discharged in atmosphere |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Temperature | Average: 298 K |
Date | May 26, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25 e/Å2 |
Tilt angle min | 0 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 85658 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 1.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC / Tilt angle max: 50 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | The particles were semi-automatically selected using EMAN2 package and manually checked. |
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CTF correction | Details: CTFFIND3 |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: OTHER / Software - Name: Spider, Relion / Number images used: 10214 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | Homologous models of GkDnaC and GkDnaI using 4NMN Chain A and 4M4W Chain O as templates respectively were docked into the reconstructed EM map. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |