+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40084 | |||||||||
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Title | E. coli clamp loader on primed template DNA | |||||||||
Map data | CLC.DNA | |||||||||
Sample |
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Keywords | clamp loader / DNA clamp / AAA+ / ATPase / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / response to radiation / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase ...DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / response to radiation / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Oakley AJ / Xu Z-Q / Dixon NE | |||||||||
Funding support | Australia, 1 items
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Citation | Journal: To Be Published Title: Structural characterisation of the complete cycle of sliding clamp loading in E. coli Authors: Xu Z-Q / Oakley AJ / Dixon NE | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40084.map.gz | 65.5 MB | EMDB map data format | |
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Header (meta data) | emd-40084-v30.xml emd-40084.xml | 27.6 KB 27.6 KB | Display Display | EMDB header |
Images | emd_40084.png | 62.8 KB | ||
Filedesc metadata | emd-40084.cif.gz | 8.2 KB | ||
Others | emd_40084_half_map_1.map.gz emd_40084_half_map_2.map.gz | 65.5 MB 65.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40084 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40084 | HTTPS FTP |
-Related structure data
Related structure data | 8gj3MC 8giyC 8gizC 8gj0C 8gj1C 8gj2C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40084.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | CLC.DNA | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: CLC.DNA half map 1
File | emd_40084_half_map_1.map | ||||||||||||
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Annotation | CLC.DNA half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CLC.DNA half map 2
File | emd_40084_half_map_2.map | ||||||||||||
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Annotation | CLC.DNA half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : E. coli clamp loader on primed template DNA
+Supramolecule #1: E. coli clamp loader on primed template DNA
+Macromolecule #1: DNA polymerase III subunit delta
+Macromolecule #2: DNA polymerase III subunit tau
+Macromolecule #3: DNA polymerase III subunit delta'
+Macromolecule #4: DNA polymerase III subunit psi
+Macromolecule #5: Primer
+Macromolecule #6: Template
+Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #8: MAGNESIUM ION
+Macromolecule #9: TETRAFLUOROALUMINATE ION
+Macromolecule #10: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 Component:
Details: 30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol. | |||||||||||||||||||||||||||
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa Details: Used a Zepto Low-pressure plasma systems (PLASMA CLEANER) (Diener Electronic) at 10% power for 120 seconds. | |||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV Details: 3 uL of sample was applied onto a Ultrafoil Au R1.2/1.3 grid. Blot for 4.5 s with no extra force before plunging into liquid ethane.. | |||||||||||||||||||||||||||
Details | 30 microL of 6.0 microM delta/tau3/delta' complex was mixed with chi/psi complex, beta, and p/t DNA (annealed DNA oligonucleotides) at a molar ratio of 1:1.3 and dialysed at 4 degrees C against 250 mL of 30 mM Tris-HCl pH 7.6, 5 mM MgCl2, 2 mM ADP, 0.5 mM AlCl3, 5 mM NaF, 5 mM dithiothreitol, 0.25 mM EDTA, 2% glycerol. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.4 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Details: unfiltered mode |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 1 / Number real images: 2909 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 645000 |
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Startup model | Type of model: OTHER / Details: Ab-initio model from RELION |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final 3D classification | Number classes: 4 / Avg.num./class: 120000 / Software - Name: RELION (ver. 3.1) Details: Most particles were classified to two classes that were used for final 3D reconstruction. |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final reconstruction | Number classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 308000 |