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Yorodumi- EMDB-16809: Cryo-EM structure of Pyrococcus furiosus transcription elongation... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16809 | |||||||||
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Title | Cryo-EM structure of Pyrococcus furiosus transcription elongation complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA / Polymerase / Elongation / Complex / Pyrococcus furiosus / Archaea / Transcription / DNA | |||||||||
Function / homology | Function and homology information 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 / magnesium ion binding / DNA binding ...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 / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Pyrococcus furiosus DSM 3638 (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Tarau DM / Reichelt R / Heiss FB / Pilsl M / Hausner W / Engel C / Grohmann D | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nucleic Acids Res. / Year: 2024 Title: Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment Authors: Tarau DM / Grunberger F / Pilsl M / Reichelt R / Heiss FB / Koenig S / Urlaub H / Hausner W / Engel C / Grohmann D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16809.map.gz | 40.8 MB | EMDB map data format | |
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Header (meta data) | emd-16809-v30.xml emd-16809.xml | 35.6 KB 35.6 KB | Display Display | EMDB header |
Images | emd_16809.png | 51.3 KB | ||
Masks | emd_16809_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-16809.cif.gz | 9.1 KB | ||
Others | emd_16809_half_map_1.map.gz emd_16809_half_map_2.map.gz | 40.9 MB 40.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16809 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16809 | HTTPS FTP |
-Related structure data
Related structure data | 8croMC 8okiC 8orqC 8p2iC 8rboC 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_16809.map.gz / Format: CCP4 / Size: 52.7 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: 1.0635 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16809_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16809_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16809_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Transcription Elongation Complex (TEC)
+Supramolecule #1: Transcription Elongation Complex (TEC)
+Supramolecule #2: Pyrococcus furiosus RNA polymerase
+Supramolecule #3: Nucleotide strands
+Macromolecule #1: DNA-directed RNA polymerase subunit Rpo1N
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit Rpo1C
+Macromolecule #4: DNA-directed RNA polymerase subunit Rpo3
+Macromolecule #5: DNA-directed RNA polymerase subunit Rpo7
+Macromolecule #6: DNA-directed RNA polymerase subunit Rpo4
+Macromolecule #7: DNA-directed RNA polymerase subunit Rpo11
+Macromolecule #8: DNA-directed RNA polymerase subunit Rpo5
+Macromolecule #9: DNA-directed RNA polymerase subunit Rpo10
+Macromolecule #10: DNA-directed RNA polymerase subunit Rpo6
+Macromolecule #11: DNA-directed RNA polymerase subunit Rpo12
+Macromolecule #12: DNA Template Strand
+Macromolecule #13: DNA Non-Template Strand
+Macromolecule #14: RNA
+Macromolecule #15: ZINC ION
+Macromolecule #16: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 88.73 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1) |
Final 3D classification | Software - Name: RELION (ver. 4.0) |
Final angle assignment | Type: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4.0) |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 333535 |