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- EMDB-0040: Structure of paused transcription complex Pol II-DSIF-NELF (Map 3) -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0040 | |||||||||
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Title | Structure of paused transcription complex Pol II-DSIF-NELF (Map 3) | |||||||||
![]() | Globally refined overall NELF-B selected particles PEC map (Map 3). | |||||||||
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Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
![]() | Vos SM / Farnung L / Urlaub H / Cramer P | |||||||||
![]() | ![]() Title: Structure of paused transcription complex Pol II-DSIF-NELF. Authors: Seychelle M Vos / Lucas Farnung / Henning Urlaub / Patrick Cramer / ![]() Abstract: Metazoan gene regulation often involves the pausing of RNA polymerase II (Pol II) in the promoter-proximal region. Paused Pol II is stabilized by the protein complexes DRB sensitivity-inducing factor ...Metazoan gene regulation often involves the pausing of RNA polymerase II (Pol II) in the promoter-proximal region. Paused Pol II is stabilized by the protein complexes DRB sensitivity-inducing factor (DSIF) and negative elongation factor (NELF). Here we report the cryo-electron microscopy structure of a paused transcription elongation complex containing Sus scrofa Pol II and Homo sapiens DSIF and NELF at 3.2 Å resolution. The structure reveals a tilted DNA-RNA hybrid that impairs binding of the nucleoside triphosphate substrate. NELF binds the polymerase funnel, bridges two mobile polymerase modules, and contacts the trigger loop, thereby restraining Pol II mobility that is required for pause release. NELF prevents binding of the anti-pausing transcription elongation factor IIS (TFIIS). Additionally, NELF possesses two flexible 'tentacles' that can contact DSIF and exiting RNA. These results define the paused state of Pol II and provide the molecular basis for understanding the function of NELF during promoter-proximal gene regulation. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.7 KB 32.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() ![]() | 9.1 KB 9.2 KB | Display Display | ![]() |
Images | ![]() | 180.5 KB | ||
Masks | ![]() ![]() ![]() | 64 MB 64 MB 64 MB | ![]() | |
Others | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 6.5 MB 49.3 MB 49.5 MB 49.5 MB 59.9 MB 49.6 MB 49.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 486.4 KB | Display | ![]() |
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Full document | ![]() | 485.5 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Globally refined overall NELF-B selected particles PEC map (Map 3). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2277 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
+Mask #1
+Mask #2
+Mask #3
+Additional map: Postprocessed/B-factor sharpened NELF-B selected particles PEC map (Map...
+Additional map: Focused refinement on NELF-ABC.
+Additional map: Half map 1 for focused refined PEC NELF-B selected particles (Map 3).
+Additional map: Half map 2 for focused refined PEC NELF-B selected particles (Map 3).
+Additional map: Postprocessed/B-factor sharpened NELF-B selected particles focused refined PEC...
+Half map: Half map 1 for globally refined PEC NELF-B...
+Half map: Half map 2 for globally refined PEC NELF-B...
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Sample components
-Entire : RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)
Entire | Name: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*) |
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Components |
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-Supramolecule #1: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*)
Supramolecule | Name: RNA Polymerase II-DSIF-PAF-SPT6 elongation complex (EC*) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21, #23 |
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Molecular weight | Theoretical: 927.1 KDa |
-Supramolecule #2: RNA Polymerase II
Supramolecule | Name: RNA Polymerase II / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#9, #11, #10, #12 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: associated proteins
Supramolecule | Name: associated proteins / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #13, #16, #18, #23, #19-#22 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #4: Nucleic acids
Supramolecule | Name: Nucleic acids / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #14-#15, #17 |
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Source (natural) | Organism: synthetic construct (others) |
Recombinant expression | Organism: synthetic construct (others) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number real images: 11740 / Average exposure time: 9.0 sec. / Average electron dose: 46.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |