+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-42304 | |||||||||
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Title | Structure of Pol II-DSIF-NELF - post-translocated | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Nucleic acids / transcription / RNA polymerase II / NELF / DSIF / pausing | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Su BG / Vos SM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2024 Title: Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing. Authors: Bonnie G Su / Seychelle M Vos / Abstract: Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF ...Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that NELF prevents Pol II elongation. Here, we report cryoelectron microscopy structures of Pol II-DSIF-NELF complexes with NELF in two distinct conformations corresponding to paused and poised states. The paused NELF state supports Pol II stalling, whereas the poised NELF state enables transcription elongation as it does not support a tilted RNA-DNA hybrid. Further, the poised NELF state can accommodate TFIIS binding to Pol II, allowing for Pol II reactivation at paused or backtracking sites. Finally, we observe that the NELF-A tentacle interacts with the RPB2 protrusion and is necessary for pausing. Our results define how NELF can support pausing, reactivation, and elongation by Pol II. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_42304.map.gz | 252.6 MB | EMDB map data format | |
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Header (meta data) | emd-42304-v30.xml emd-42304.xml | 34 KB 34 KB | Display Display | EMDB header |
Images | emd_42304.png | 161.9 KB | ||
Masks | emd_42304_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-42304.cif.gz | 10.1 KB | ||
Others | emd_42304_additional_1.map.gz emd_42304_half_map_1.map.gz emd_42304_half_map_2.map.gz | 245.3 MB 418.2 MB 411.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-42304 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-42304 | HTTPS FTP |
-Validation report
Summary document | emd_42304_validation.pdf.gz | 929.5 KB | Display | EMDB validaton report |
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Full document | emd_42304_full_validation.pdf.gz | 929 KB | Display | |
Data in XML | emd_42304_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | emd_42304_validation.cif.gz | 22.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42304 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-42304 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_42304.map.gz / Format: CCP4 / Size: 512 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: 0.822 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_42304_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_42304_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42304_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_42304_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA Polymerase in complex with DSIF and NELF
+Supramolecule #1: RNA Polymerase in complex with DSIF and NELF
+Macromolecule #1: RPB1
+Macromolecule #2: RPB2
+Macromolecule #3: RPB3
+Macromolecule #4: RPB4
+Macromolecule #5: RPB5
+Macromolecule #6: RPB6
+Macromolecule #7: RPB7
+Macromolecule #8: RPB8
+Macromolecule #9: RPB9
+Macromolecule #10: RPB10
+Macromolecule #11: RPB11
+Macromolecule #12: RPB12
+Macromolecule #16: NELF-A
+Macromolecule #17: SPT4
+Macromolecule #18: SPT5
+Macromolecule #19: NELF-C
+Macromolecule #20: NELF-B
+Macromolecule #21: NELF-E
+Macromolecule #13: Non-template DNA
+Macromolecule #15: Template DNA
+Macromolecule #14: RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50535 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |