+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0038 | ||||||||||||
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Title | Structure of paused transcription complex Pol II-DSIF-NELF | ||||||||||||
Map data | Globally refined overall PEC map (Map 1). | ||||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of protein modification process / NELF complex / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination ...positive regulation of protein modification process / NELF complex / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / negative regulation of stem cell differentiation / nuclear-transcribed mRNA catabolic process, exonucleolytic / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / : / positive regulation of DNA-templated transcription, elongation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / organelle membrane / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of translational initiation / positive regulation of macroautophagy / Tat-mediated elongation of the HIV-1 transcript / transcription-coupled nucleotide-excision repair / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / localization / RNA polymerase I complex / RNA polymerase III complex / transcription by RNA polymerase I / transcription by RNA polymerase III / RNA Polymerase II Transcription Elongation / RNA polymerase II, core complex / Formation of RNA Pol II elongation complex / translation initiation factor binding / core promoter sequence-specific DNA binding / RNA Polymerase II Pre-transcription Events / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / stem cell differentiation / P-body / euchromatin / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / chromatin organization / cell population proliferation / single-stranded RNA binding / chromosome, telomeric region / transcription by RNA polymerase II / nucleic acid binding / positive regulation of ERK1 and ERK2 cascade / molecular adaptor activity / protein dimerization activity / nuclear body / nuclear speck / protein heterodimerization activity / nucleotide binding / mRNA binding / DNA-templated transcription Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Human immunodeficiency virus 1 / Pig (pig) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Vos SM / Farnung L / Urlaub H / Cramer P | ||||||||||||
Funding support | Germany, 3 items
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Citation | Journal: Nature / Year: 2018 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0038.map.gz | 49.7 MB | EMDB map data format | |
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Header (meta data) | emd-0038-v30.xml emd-0038.xml | 48 KB 48 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0038_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_0038.png | 192.2 KB | ||
Masks | emd_0038_msk_1.map | 64 MB | Mask map | |
Others | emd_0038_additional.map.gz emd_0038_half_map_1.map.gz emd_0038_half_map_2.map.gz | 7.7 MB 49.6 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0038 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0038 | HTTPS FTP |
-Related structure data
Related structure data | 6gmlMC 0039C 0040C 0041C 0042C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0038.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Globally refined overall PEC map (Map 1). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
File | emd_0038_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Postprocessed/B-factor sharpened overall PEC map (Map 1). Applied...
File | emd_0038_additional.map | ||||||||||||
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Annotation | Postprocessed/B-factor sharpened overall PEC map (Map 1). Applied B-factor of -65. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 for globally refined PEC (Map 1).
File | emd_0038_half_map_1.map | ||||||||||||
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Annotation | Half map 1 for globally refined PEC (Map 1). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 for globally refined PEC (Map 1).
File | emd_0038_half_map_2.map | ||||||||||||
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Annotation | Half map 2 for globally refined PEC (Map 1). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA Polymerase II elongation complex bound to DSIF and NELF
+Supramolecule #1: RNA Polymerase II elongation complex bound to DSIF and NELF
+Supramolecule #2: Sus scrofa RNA Polymerase II
+Supramolecule #3: Negative elongation factor (NELF)
+Supramolecule #4: DRB sensitivity inducing factor (DSIF)
+Supramolecule #5: HIV-1 pause transcription scaffold
+Macromolecule #1: DNA-directed RNA polymerase subunit
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: RNA polymerase II subunit C
+Macromolecule #4: RNA polymerase II subunit E
+Macromolecule #5: RNA polymerase II subunit F
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #8: Uncharacterized protein
+Macromolecule #9: Uncharacterized protein
+Macromolecule #10: Uncharacterized protein
+Macromolecule #14: Negative elongation factor A
+Macromolecule #15: Negative elongation factor B,Negative elongation factor B
+Macromolecule #16: Negative elongation factor C/D
+Macromolecule #17: Negative elongation factor E,Negative elongation factor E
+Macromolecule #18: Transcription elongation factor SPT4
+Macromolecule #19: Transcription elongation factor SPT5
+Macromolecule #20: RNA polymerase II subunit D
+Macromolecule #21: RNA polymerase II subunit G
+Macromolecule #11: Non-template DNA
+Macromolecule #13: Template DNA
+Macromolecule #12: TAR RNA
+Macromolecule #22: MAGNESIUM ION
+Macromolecule #23: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 165000 |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |