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Yorodumi- EMDB-9970: Thermococcus kodakarensis RNA polymerase in complex with transcri... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9970 | |||||||||||||||
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Title | Thermococcus kodakarensis RNA polymerase in complex with transcription factor E and promoter DNA, focused refinement on RNAP stalk and clamp domains and TFE | |||||||||||||||
Map data | Cryo-EM single particle analysis 3D reconstruction of RNA polymerase (RNAP) from Thermococcus kodakarensis (Tko) in complex with transcription factor E (TFE) and DNA, focused refinement | |||||||||||||||
Sample |
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Function / homology | Function and homology information transcription open complex formation at RNA polymerase II promoter / DNA-directed RNA polymerase complex / 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 ...transcription open complex formation at RNA polymerase II promoter / DNA-directed RNA polymerase complex / 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 | Thermococcus kodakarensis KOD1 (archaea) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.85 Å | |||||||||||||||
Authors | Hyun J / Jun S-H / Cho H-S / Murakami KS | |||||||||||||||
Funding support | United States, Korea, Republic Of, 4 items
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Citation | Journal: To Be Published 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9970.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-9970-v30.xml emd-9970.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_9970_fsc.xml | 6.3 KB | Display | FSC data file |
Images | emd_9970.png | 129.5 KB | ||
Masks | emd_9970_msk_1.map | 20.8 MB | Mask map | |
Others | emd_9970_half_map_1.map.gz emd_9970_half_map_2.map.gz | 15.5 MB 15.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9970 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9970 | HTTPS FTP |
-Related structure data
Related structure data | 6kf9M 9960C 9961C 9962C 9969C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9970.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 DNA, focused refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | emd_9970_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Tko RNAP-TFE-DNA (focused refinement) half map 1
File | emd_9970_half_map_1.map | ||||||||||||
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Annotation | Tko RNAP-TFE-DNA (focused refinement) half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Tko RNAP-TFE-DNA (focused refinement) half map 2
File | emd_9970_half_map_2.map | ||||||||||||
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Annotation | Tko RNAP-TFE-DNA (focused refinement) half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-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: Thermococcus kodakarensis KOD1 (archaea) |
Molecular weight | Theoretical: 410 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.002 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 47000 |
Specialist optics | Spherical aberration corrector: Image Cs corrector |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |