[English] 日本語
Yorodumi- PDB-6ted: Structure of complete, activated transcription complex Pol II-DSI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ted | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1 | |||||||||||||||
Components |
| |||||||||||||||
Keywords | TRANSCRIPTION / Polymerase / elongation complex / RNA / DNA | |||||||||||||||
Function / homology | Function and homology information blastocyst growth / inner cell mass cell differentiation / positive regulation of mRNA 3'-end processing / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / mRNA decay by 3' to 5' exoribonuclease / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / regulation of isotype switching / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay ...blastocyst growth / inner cell mass cell differentiation / positive regulation of mRNA 3'-end processing / Ski complex / RNA polymerase II C-terminal domain phosphoserine binding / mRNA decay by 3' to 5' exoribonuclease / negative regulation of DNA-templated transcription, elongation / Cdc73/Paf1 complex / regulation of isotype switching / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / regulation of muscle cell differentiation / regulation of mRNA export from nucleus / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / : / DSIF complex / positive regulation of cell cycle G1/S phase transition / blastocyst hatching / trophectodermal cell differentiation / regulation of mRNA processing / regulation of transcription elongation by RNA polymerase II / nucleosome organization / 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 - 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 / mRNA Splicing - Major Pathway / blastocyst formation / mRNA 3'-end processing / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / stem cell population maintenance / transcription elongation-coupled chromatin remodeling / negative regulation of G1/S transition of mitotic cell cycle / 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 / organelle membrane / interleukin-6-mediated signaling pathway / mRNA Capping / negative regulation of gene expression, epigenetic / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase III activity / RNA polymerase II complex binding / negative regulation of 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 / RNA polymerase II transcribes snRNA genes / positive regulation of macroautophagy / positive regulation of Wnt signaling pathway / RNA polymerase II activity / nucleosome binding / protein localization to nucleus / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / mRNA transport / tRNA transcription by RNA polymerase III / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / RNA Polymerase II Pre-transcription Events / translation initiation factor binding / SH2 domain binding Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) Sus scrofa (pig) synthetic construct (others) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Vos, S.M. / Farnung, L. / Cramer, P. | |||||||||||||||
Funding support | Germany, 4items
| |||||||||||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6ted.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ted.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6ted.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ted_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ted_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6ted_validation.xml.gz | 214.9 KB | Display | |
Data in CIF | 6ted_validation.cif.gz | 337.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/te/6ted ftp://data.pdbj.org/pub/pdb/validation_reports/te/6ted | HTTPS FTP |
-Related structure data
Related structure data | 10480MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-DNA-directed RNA polymerase ... , 3 types, 3 molecules ABI
#1: Protein | Mass: 219049.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: A0A480RVL6, DNA-directed RNA polymerase |
---|---|
#2: Protein | Mass: 142426.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899 |
-RNA polymerase II subunit ... , 5 types, 5 molecules CDEFG
#3: Protein | Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3 |
---|---|
#4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4 |
#5: Protein | Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LSI7 |
#6: Protein | Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKN8 |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LJZ9 |
-Protein , 4 types, 4 molecules HVWX
#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCB2 |
---|---|
#20: Protein | Mass: 60052.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAF1, PD2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N7H5 |
#21: Protein | Mass: 33617.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR61 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9GZS3 |
#22: Protein | Mass: 60673.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC73, C1orf28, HRPT2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P1J9 |
-Uncharacterized ... , 3 types, 3 molecules JKL
#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B432, UniProt: A0A4X1VYD0*PLUS |
---|---|
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RKE4 |
#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LN51 |
-Transcription elongation factor ... , 3 types, 3 molecules MYZ
#13: Protein | Mass: 199602.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT6H, KIAA0162, SPT6H / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q7KZ85 |
---|---|
#23: Protein | Mass: 13508.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT4H1, SPT4H, SUPT4H / Production host: Escherichia coli (E. coli) / References: UniProt: P63272 |
#24: Protein | Mass: 121225.477 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli (E. coli) / References: UniProt: O00267 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 14932.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#18: DNA chain | Mass: 14672.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-RNA chain , 1 types, 1 molecules P
#15: RNA chain | Mass: 14843.892 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|
-RNA polymerase-associated protein ... , 3 types, 3 molecules QRU
#16: Protein | Mass: 134510.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTR9, KIAA0155, SH2BP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6PD62 |
---|---|
#17: Protein | Mass: 80733.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RTF1, KIAA0252 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92541 |
#19: Protein | Mass: 75514.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LEO1, RDL / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WVC0 |
-Non-polymers , 2 types, 10 molecules
#25: Chemical | ChemComp-ZN / #26: Chemical | ChemComp-MG / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 1.34 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil | ||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: 2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 13679 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 611983 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 446195 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 115 / Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|