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Yorodumi- EMDB-44649: Cryo-EM structure of Thermococcus kodakarensis FttA-dependent tra... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-44649 | |||||||||
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Title | Cryo-EM structure of Thermococcus kodakarensis FttA-dependent transcription pre-termination complex containing 44 nt RNA (local refinement map) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA polymerase / pre-termination complex / FttA / archaea / TRANSCRIPTION | |||||||||
Biological species | Thermococcus kodakarensis (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.67 Å | |||||||||
Authors | You L / Ebright RH | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Structural basis of archaeal FttA-dependent transcription termination Authors: You L / Ebright RH | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_44649.map.gz | 122.4 MB | EMDB map data format | |
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Header (meta data) | emd-44649-v30.xml emd-44649.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_44649_fsc.xml | 13.2 KB | Display | FSC data file |
Images | emd_44649.png | 58.5 KB | ||
Filedesc metadata | emd-44649.cif.gz | 4 KB | ||
Others | emd_44649_half_map_1.map.gz emd_44649_half_map_2.map.gz | 226.5 MB 226.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-44649 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-44649 | HTTPS FTP |
-Validation report
Summary document | emd_44649_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_44649_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_44649_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | emd_44649_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44649 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-44649 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_44649.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.825 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_44649_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_44649_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : FttA-dependent transcription termination complex
Entire | Name: FttA-dependent transcription termination complex |
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Components |
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-Supramolecule #1: FttA-dependent transcription termination complex
Supramolecule | Name: FttA-dependent transcription termination complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17 |
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Source (natural) | Organism: Thermococcus kodakarensis (archaea) |
Molecular weight | Theoretical: 556 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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