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Yorodumi- EMDB-19033: Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19033 | |||||||||
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Title | Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase contracted clamp conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | RNA / Polymerase / Elongation / Complex / Pyrococcus furiosus / Archaea / Transcription / DNA | |||||||||
Function / homology | Function and homology information RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...RNA polymerase III activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / 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 / DNA-templated transcription / nucleotide binding / 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: 3.02 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: Daniela Tarău / Felix Grünberger / Michael Pilsl / Robert Reichelt / Florian Heiß / Sabine König / Henning Urlaub / Winfried Hausner / Christoph Engel / Dina Grohmann / Abstract: Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, ...Archaeal transcription is carried out by a multi-subunit RNA polymerase (RNAP) that is highly homologous in structure and function to eukaryotic RNAP II. Among the set of basal transcription factors, only Spt5 is found in all domains of life, but Spt5 has been shaped during evolution, which is also reflected in the heterodimerization of Spt5 with Spt4 in Archaea and Eukaryotes. To unravel the mechanistic basis of Spt4/5 function in Archaea, we performed structure-function analyses using the archaeal transcriptional machinery of Pyrococcus furiosus (Pfu). We report single-particle cryo-electron microscopy reconstructions of apo RNAP and the archaeal elongation complex (EC) in the absence and presence of Spt4/5. Surprisingly, Pfu Spt4/5 also binds the RNAP in the absence of nucleic acids in a distinct super-contracted conformation. We show that the RNAP clamp/stalk module exhibits conformational flexibility in the apo state of RNAP and that the enzyme contracts upon EC formation or Spt4/5 engagement. We furthermore identified a contact of the Spt5-NGN domain with the DNA duplex that stabilizes the upstream boundary of the transcription bubble and impacts Spt4/5 activity in vitro. This study, therefore, provides the structural basis for Spt4/5 function in archaeal transcription and reveals a potential role beyond the well-described support of elongation. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19033.map.gz | 51.7 MB | EMDB map data format | |
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Header (meta data) | emd-19033-v30.xml emd-19033.xml | 28.7 KB 28.7 KB | Display Display | EMDB header |
Images | emd_19033.png | 57.8 KB | ||
Masks | emd_19033_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-19033.cif.gz | 8.1 KB | ||
Others | emd_19033_half_map_1.map.gz emd_19033_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19033 | HTTPS FTP |
-Validation report
Summary document | emd_19033_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_19033_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_19033_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_19033_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19033 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19033 | HTTPS FTP |
-Related structure data
Related structure data | 8rboMC 8croC 8okiC 8orqC 8p2iC 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_19033.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.968 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19033_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19033_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19033_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Pyrococcus furiosus apo form of RNA polymerase contracted clamp c...
+Supramolecule #1: Pyrococcus furiosus apo form of RNA polymerase contracted clamp c...
+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 Rpo5
+Macromolecule #8: DNA-directed RNA polymerase subunit Rpo6
+Macromolecule #9: DNA-directed RNA polymerase subunit Rpo11
+Macromolecule #10: DNA-directed RNA polymerase subunit Rpo10
+Macromolecule #11: DNA-directed RNA polymerase subunit Rpo12
+Macromolecule #12: ZINC ION
+Macromolecule #13: 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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | JEOL CRYO ARM 200 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111194 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |