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- EMDB-40081: E. coli clamp loader with open clamp on primed template DNA (form 1) -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | E. coli clamp loader with open clamp on primed template DNA (form 1) | |||||||||
![]() | CLC.DNA.Beta2 Open1 | |||||||||
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![]() | clamp loader / DNA clamp / AAA+ / ATPase / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | ![]() DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA clamp loader activity / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity ...DNA polymerase III, clamp loader complex / Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA clamp loader activity / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA polymerase processivity factor activity / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 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 / DNA repair / DNA damage response / protein homodimerization activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Oakley AJ / Xu Z-Q / Dixon NE | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 140.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 29.6 KB 29.6 KB | Display Display | ![]() |
Images | ![]() | 47.4 KB | ||
Filedesc metadata | ![]() | 8.5 KB | ||
Others | ![]() ![]() | 140.7 MB 140.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 869.5 KB | Display | ![]() |
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Full document | ![]() | 869.1 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 17.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8gj0MC ![]() 8giyC ![]() 8gizC ![]() 8gj1C ![]() 8gj2C ![]() 8gj3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | CLC.DNA.Beta2 Open1 | ||||||||||||||||||||
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.Beta2 Open1 half map 1
File | emd_40081_half_map_1.map | ||||||||||||
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Annotation | CLC.DNA.Beta2 Open1 half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: CLC.DNA.Beta2 Open1 half map 2
File | emd_40081_half_map_2.map | ||||||||||||
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Annotation | CLC.DNA.Beta2 Open1 half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : E. coli clamp loader with open clamp on primed template DNA
+Supramolecule #1: E. coli clamp loader with open clamp 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: Beta sliding clamp
+Macromolecule #6: Primer
+Macromolecule #7: Template
+Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
+Macromolecule #10: TETRAFLUOROALUMINATE ION
+Macromolecule #11: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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 / Support film - Material: GOLD / 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. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Details: unfiltered mode |
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: 4226 / Average exposure time: 6.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.4 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |