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Yorodumi- EMDB-10480: Structure of complete, activated transcription complex Pol II-DSI... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10480 | |||||||||||||||
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Title | Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1 (Map 1) | |||||||||||||||
Map data | B factor of -115 applied | |||||||||||||||
Sample |
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Function / homology | Function and homology information blastocyst growth / inner cell mass cell differentiation / Ski complex / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of isotype switching ...blastocyst growth / inner cell mass cell differentiation / Ski complex / positive regulation of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / RNA polymerase II C-terminal domain phosphoserine binding / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of isotype switching / regulation of muscle cell differentiation / endodermal cell fate commitment / regulation of mRNA export from nucleus / negative regulation of myeloid cell differentiation / blastocyst hatching / : / positive regulation of cell cycle G1/S phase transition / DSIF complex / trophectodermal cell differentiation / regulation of mRNA processing / nucleosome organization / 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 / blastocyst formation / mRNA 3'-end processing / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / negative regulation of G1/S transition of mitotic cell cycle / organelle membrane / stem cell population maintenance / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / interleukin-6-mediated signaling pathway / negative regulation of gene expression, epigenetic / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / RNA polymerase III activity / negative regulation of transcription elongation by RNA polymerase II / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / transcription by RNA polymerase I / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / cell surface receptor signaling pathway via JAK-STAT / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / positive regulation of macroautophagy / RNA polymerase II transcribes snRNA genes / RNA polymerase II activity / protein localization to nucleus / positive regulation of Wnt signaling pathway / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / mRNA transport / tRNA transcription by RNA polymerase III / RNA polymerase I activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / nucleosome binding / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / positive regulation of transcription elongation by RNA polymerase II / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / translation initiation factor binding / RNA Polymerase II Pre-transcription Events Similarity search - Function | |||||||||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / synthetic construct (others) / Pig (pig) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Vos SM / Farnung L / Cramer P | |||||||||||||||
Funding support | Germany, 4 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Structure of complete Pol II-DSIF-PAF-SPT6 transcription complex reveals RTF1 allosteric activation. Authors: Seychelle M Vos / Lucas Farnung / Andreas Linden / Henning Urlaub / Patrick Cramer / Abstract: Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation ...Transcription by RNA polymerase II (Pol II) is carried out by an elongation complex. We previously reported an activated porcine Pol II elongation complex, EC*, encompassing the human elongation factors DSIF, PAF1 complex (PAF) and SPT6. Here we report the cryo-EM structure of the complete EC* that contains RTF1, a dissociable PAF subunit critical for chromatin transcription. The RTF1 Plus3 domain associates with Pol II subunit RPB12 and the phosphorylated C-terminal region of DSIF subunit SPT5. RTF1 also forms four α-helices that extend from the Plus3 domain along the Pol II protrusion and RPB10 to the polymerase funnel. The C-terminal 'fastener' helix retains PAF and is followed by a 'latch' that reaches the end of the bridge helix, a flexible element of the Pol II active site. RTF1 strongly stimulates Pol II elongation, and this requires the latch, possibly suggesting that RTF1 activates transcription allosterically by influencing Pol II translocation. | |||||||||||||||
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_10480.map.gz | 160.3 MB | EMDB map data format | |
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Header (meta data) | emd-10480-v30.xml emd-10480.xml | 56.6 KB 56.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10480_fsc.xml | 12.8 KB | Display | FSC data file |
Images | emd_10480.png | 168.3 KB | ||
Masks | emd_10480_msk_1.map emd_10480_msk_2.map | 178 MB 178 MB | Mask map | |
Others | emd_10480_additional.map.gz emd_10480_half_map_1.map.gz emd_10480_half_map_2.map.gz | 158.8 MB 139.7 MB 139.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10480 | HTTPS FTP |
-Validation report
Summary document | emd_10480_validation.pdf.gz | 439.4 KB | Display | EMDB validaton report |
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Full document | emd_10480_full_validation.pdf.gz | 438.5 KB | Display | |
Data in XML | emd_10480_validation.xml.gz | 18.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10480 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10480 | HTTPS FTP |
-Related structure data
Related structure data | 6tedMC 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_10480.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | B factor of -115 applied | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.049 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_10480_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_10480_msk_2.map | ||||||||||||
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Density Histograms |
-Additional map: Composite map used for model refinement. Generated using maps 1, 2,
File | emd_10480_additional.map | ||||||||||||
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Annotation | Composite map used for model refinement. Generated using maps 1, 2, | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_10480_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_10480_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complete EC*
+Supramolecule #1: Complete EC*
+Supramolecule #2: Pig DNA/RNA polymerase subunits
+Supramolecule #3: Human transcription factors and associated proteins
+Supramolecule #4: DNA/RNA
+Supramolecule #5: Transcription elongation factor SPT4 and SPT5
+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 D
+Macromolecule #5: RNA polymerase II subunit E
+Macromolecule #6: RNA polymerase II subunit F
+Macromolecule #7: RNA polymerase II subunit G
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: Uncharacterized protein
+Macromolecule #11: Uncharacterized protein
+Macromolecule #12: Uncharacterized protein
+Macromolecule #13: Transcription elongation factor SPT6
+Macromolecule #16: RNA polymerase-associated protein CTR9 homolog
+Macromolecule #17: RNA polymerase-associated protein RTF1 homolog
+Macromolecule #19: RNA polymerase-associated protein LEO1
+Macromolecule #20: RNA polymerase II-associated factor 1 homolog
+Macromolecule #21: WD repeat-containing protein 61
+Macromolecule #22: Parafibromin
+Macromolecule #23: Transcription elongation factor SPT4
+Macromolecule #24: Transcription elongation factor SPT5
+Macromolecule #14: DNA (37-MER)
+Macromolecule #18: Template DNA
+Macromolecule #15: RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP...
+Macromolecule #25: ZINC ION
+Macromolecule #26: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Number real images: 13679 / Average exposure time: 10.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |