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Yorodumi- EMDB-0242: Yeast RNA polymerase I elongation complex bound to nucleotide ana... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0242 | |||||||||
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Title | Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map) | |||||||||
Map data | Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map) | |||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Tafur L / Sadian Y / Weis F / Muller CW | |||||||||
Citation | Journal: Elife / Year: 2019 Title: The cryo-EM structure of a 12-subunit variant of RNA polymerase I reveals dissociation of the A49-A34.5 heterodimer and rearrangement of subunit A12.2. Authors: Lucas Tafur / Yashar Sadian / Jonas Hanske / Rene Wetzel / Felix Weis / Christoph W Müller / Abstract: RNA polymerase (Pol) I is a 14-subunit enzyme that solely transcribes pre-ribosomal RNA. Cryo-electron microscopy (EM) structures of Pol I initiation and elongation complexes have given first ...RNA polymerase (Pol) I is a 14-subunit enzyme that solely transcribes pre-ribosomal RNA. Cryo-electron microscopy (EM) structures of Pol I initiation and elongation complexes have given first insights into the molecular mechanisms of Pol I transcription. Here, we present cryo-EM structures of yeast Pol I elongation complexes (ECs) bound to the nucleotide analog GMPCPP at 3.2 to 3.4 Å resolution that provide additional insight into the functional interplay between the Pol I-specific transcription-like factors A49-A34.5 and A12.2. Strikingly, most of the nucleotide-bound ECs lack the A49-A34.5 heterodimer and adopt a Pol II-like conformation, in which the A12.2 C-terminal domain is bound in a previously unobserved position at the A135 surface. Our structural and biochemical data suggest a mechanism where reversible binding of the A49-A34.5 heterodimer could contribute to the regulation of Pol I transcription initiation and elongation. | |||||||||
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_0242.map.gz | 51.9 MB | EMDB map data format | |
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Header (meta data) | emd-0242-v30.xml emd-0242.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0242_fsc.xml | 10.8 KB | Display | FSC data file |
Images | emd_0242.png | 68 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0242 | HTTPS FTP |
-Related structure data
Related structure data | 0238C 0239C 0240C 0241C 6hkoC 6hlqC 6hlrC 6hlsC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0242.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Yeast RNA polymerase I elongation complex bound to nucleotide ana...
Entire | Name: Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map) |
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Components |
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-Supramolecule #1: Yeast RNA polymerase I elongation complex bound to nucleotide ana...
Supramolecule | Name: Yeast RNA polymerase I elongation complex bound to nucleotide analog GMPCPP (upstream DNA focused, unsharpened map) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 30 seconds incubation 3 seconds blotting blotting force 3. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | Initial rigid body fitting was done in Chimera and model building was done in Coot. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |