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- EMDB-9962: Thermococcus kodakarensis RNA polymerase in complex with transcri... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9962 | |||||||||||||||
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Title | Thermococcus kodakarensis RNA polymerase in complex with transcription factor E and promoter DNA | |||||||||||||||
![]() | Cryo-EM single particle analysis 3D reconstruction of RNA polymerase (RNAP) from Thermococcus kodakarensis (Tko), in complex with transcription factor E (TFE) and promotor DNA | |||||||||||||||
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Function / homology | ![]() transcription open complex formation at RNA polymerase II promoter / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...transcription open complex formation at RNA polymerase II promoter / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / nucleotide binding / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
![]() | Hyun J / Jun S-H / Cho H-S / Murakami KS | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Thermococcus kodakraensis RNA polymerase in apo form Authors: Hyun J / Jun S-H / Cho H-S / Murakami KS | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.2 KB 19.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.3 KB | Display | ![]() |
Images | ![]() | 112.5 KB | ||
Masks | ![]() | 20.8 MB | ![]() | |
Others | ![]() ![]() | 15.6 MB 15.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 488.2 KB | Display | ![]() |
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Full document | ![]() | 487.8 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kf9M ![]() 9960C ![]() 9961C ![]() 9969C ![]() 9970C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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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 | Cryo-EM single particle analysis 3D reconstruction of RNA polymerase (RNAP) from Thermococcus kodakarensis (Tko), in complex with transcription factor E (TFE) and promotor DNA | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Tko RNAP-TFE-DNA halfmap 1
File | emd_9962_half_map_1.map | ||||||||||||
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Annotation | Tko RNAP-TFE-DNA halfmap 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Tko RNAP-TFE-DNA halfmap 2
File | emd_9962_half_map_2.map | ||||||||||||
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Annotation | Tko RNAP-TFE-DNA halfmap 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Thermococcus kodakarensis RNA polymerase in complex with transcri...
Entire | Name: Thermococcus kodakarensis RNA polymerase in complex with transcription factor E and promoter DNA |
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Components |
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-Supramolecule #1: Thermococcus kodakarensis RNA polymerase in complex with transcri...
Supramolecule | Name: Thermococcus kodakarensis RNA polymerase in complex with transcription factor E and promoter DNA type: complex / ID: 1 / Parent: 0 Details: RNA polymerase from euryarchaea (Thermococcus kodakarensis) composed of 11 subunits (Rpo1', Rpo1", Rpo2, Rpo3, Rpo4, Rpo5, Rpo6, Rpo7, Rpo10, Rpo11, Rpo12), and in complex with transcription ...Details: RNA polymerase from euryarchaea (Thermococcus kodakarensis) composed of 11 subunits (Rpo1', Rpo1", Rpo2, Rpo3, Rpo4, Rpo5, Rpo6, Rpo7, Rpo10, Rpo11, Rpo12), and in complex with transcription factor E and promoter DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 410 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: GRAPHENE OXIDE / Support film - #1 - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 26.0 kPa Details: Due to preferred orientation of the particles, one dataset was collected using holey carbon EM grid, and another dataset was collected from holey carbon grid coated with graphene oxide. Note ...Details: Due to preferred orientation of the particles, one dataset was collected using holey carbon EM grid, and another dataset was collected from holey carbon grid coated with graphene oxide. Note that graphene oxide-coated grid was not pre-treated with glow discharge. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: Image Cs corrector |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-30 / Number real images: 3754 / Average exposure time: 1.8 sec. / Average electron dose: 63.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.002 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |