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Yorodumi- PDB-7okx: Structure of active transcription elongation complex Pol II-DSIF ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7okx | |||||||||||||||
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Title | Structure of active transcription elongation complex Pol II-DSIF (SPT5-KOW5)-ELL2-EAF1 (composite structure) | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION / Pol II / Super elongation complex / ELL2 / EAF1 | |||||||||||||||
Function / homology | Function and homology information super elongation complex / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / snRNA transcription by RNA polymerase II / transcription elongation factor activity / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination ...super elongation complex / negative regulation of DNA-templated transcription, elongation / DSIF complex / regulation of transcription elongation by RNA polymerase II / snRNA transcription by RNA polymerase II / transcription elongation factor activity / 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 / : / 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 / intercellular bridge / 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 / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / RNA polymerase II activity / organelle membrane / positive regulation of translational initiation / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / positive regulation of macroautophagy / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase I / RNA polymerase I complex / RNA polymerase III complex / transcription by RNA polymerase III / Formation of HIV elongation complex in the absence of HIV Tat / Cajal body / RNA polymerase II, core complex / cis-regulatory region sequence-specific DNA binding / RNA Polymerase II Transcription Elongation / translation initiation factor binding / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription elongation factor complex / positive regulation of RNA splicing / DNA-directed RNA polymerase complex / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / P-body / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / single-stranded DNA binding / chromosome / single-stranded RNA binding / chromosome, telomeric region / transcription by RNA polymerase II / nucleic acid binding / protein dimerization activity / nuclear body / nuclear speck / protein heterodimerization activity / nucleotide binding / intracellular membrane-bounded organelle / mRNA binding / DNA-templated transcription / chromatin binding / nucleolus Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) HIV whole-genome vector AA1305#18 (others) Sus scrofa (pig) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||
Authors | Chen, Y. / Vos, S.M. / Dienemann, C. / Ninov, M. / Urlaub, H. / Cramer, P. | |||||||||||||||
Funding support | Germany, 4items
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Citation | Journal: Mol Cell / Year: 2021 Title: Allosteric transcription stimulation by RNA polymerase II super elongation complex. Authors: Ying Chen / Seychelle M Vos / Christian Dienemann / Momchil Ninov / Henning Urlaub / Patrick Cramer / Abstract: The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we ...The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft. | |||||||||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7okx.cif.gz | 833.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7okx.ent.gz | 654.8 KB | Display | PDB format |
PDBx/mmJSON format | 7okx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ok/7okx ftp://data.pdbj.org/pub/pdb/validation_reports/ok/7okx | HTTPS FTP |
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-Related structure data
Related structure data | 12969MC 7okyC 7ol0C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase II subunit ... , 6 types, 6 molecules ACEFGI
#1: Protein | Mass: 217450.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P11414 |
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#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 |
#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 |
#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 |
-Protein , 5 types, 5 molecules BKMOZ
#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 |
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#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1UK25 |
#13: Protein | Mass: 72435.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ELL2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O00472 |
#15: Protein | Mass: 29075.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EAF1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96JC9 |
#18: Protein | Mass: 121145.477 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 BL21(DE3) (bacteria) / References: UniProt: O00267 |
-RNA polymerase II subunit ... , 2 types, 2 molecules DL
#4: Protein | Mass: 20962.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4 |
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#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 |
-DNA-directed RNA polymerases I, II, and III subunit ... , 2 types, 2 molecules HJ
#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1ULF2 |
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#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYD0 |
-DNA chain , 2 types, 2 molecules NT
#14: DNA chain | Mass: 14672.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others) Production host: synthetic construct |
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#17: DNA chain | Mass: 14934.580 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others) Production host: synthetic construct |
-RNA chain , 1 types, 1 molecules P
#16: RNA chain | Mass: 15076.017 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The last nucleotide (A47) was extended at the 3' of the original RNA scaffold (46-mer) during complex assembly in the presence of ATP. Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others) Production host: synthetic construct |
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-Non-polymers , 2 types, 9 molecules
#19: Chemical | ChemComp-MG / |
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#20: Chemical | ChemComp-ZN / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 43.21 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 364641 Details: This is a composite map of three focused maps: map 5, 6, and 7. Symmetry type: POINT |
Atomic model building | Space: REAL |