+Open data
-Basic information
Entry | Database: PDB / ID: 8rc4 | ||||||||||||
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Title | Structure of Integrator-PP2A complex | ||||||||||||
Components |
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Keywords | TRANSCRIPTION / Integrator complex / Post-termination complex / RNA Polymerase II / Pol II / RNAPII | ||||||||||||
Function / homology | Function and homology information regulation of fertilization / U2 snRNA 3'-end processing / snRNA processing / integrator complex / snRNA 3'-end processing / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression ...regulation of fertilization / U2 snRNA 3'-end processing / snRNA processing / integrator complex / snRNA 3'-end processing / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / flagellated sperm motility / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation / protein localization to nuclear envelope / regulation of transcription elongation by RNA polymerase II / peptidyl-threonine dephosphorylation / : / positive regulation of microtubule binding / negative regulation of tyrosine phosphorylation of STAT protein / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein antigen binding / protein phosphatase regulator activity / ceramide metabolic process / GABA receptor binding / negative regulation of epithelial to mesenchymal transition / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / regulation of Wnt signaling pathway / Disassembly of the destruction complex and recruitment of AXIN to the membrane / regulation of growth / centrosome localization / inner cell mass cell proliferation / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / protein serine/threonine phosphatase activity / CTLA4 inhibitory signaling / Platelet sensitization by LDL / negative regulation of MAPK cascade / protein-serine/threonine phosphatase / regulation of cell differentiation / T cell homeostasis / ERK/MAPK targets / regulation of G1/S transition of mitotic cell cycle / regulation of DNA replication / phosphoprotein phosphatase activity / mesoderm development / RNA polymerase II transcribes snRNA genes / chromosome, centromeric region / DARPP-32 events / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of cell adhesion / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RNA endonuclease activity / embryo implantation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / AURKA Activation by TPX2 / protein dephosphorylation / mitotic spindle organization / RNA splicing / meiotic cell cycle / DNA damage checkpoint signaling / response to organic substance / protein tyrosine phosphatase activity / chromosome segregation / RHO GTPases Activate Formins / cellular response to ionizing radiation / response to lead ion / regulation of protein phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / Spry regulation of FGF signaling / RAF activation / tau protein binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Trichoplusia ni (cabbage looper) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Fianu, I. / Ochmann, M. / Walshe, J.L. / Cramer, P. | ||||||||||||
Funding support | Germany, European Union, 3items
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Citation | Journal: Nature / Year: 2024 Title: Structural basis of Integrator-dependent RNA polymerase II termination. Authors: Isaac Fianu / Moritz Ochmann / James L Walshe / Olexandr Dybkov / Joseph Neos Cruz / Henning Urlaub / Patrick Cramer / Abstract: The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex ...The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript, but has not explained how Integrator removes Pol II from the DNA template. Here we present three cryo-electron microscopy structures of the complete Integrator-PP2A complex in different functional states. The structure of the pre-termination complex reveals a previously unresolved, scorpion-tail-shaped INTS10-INTS13-INTS14-INTS15 module that may use its 'sting' to open the DSIF DNA clamp and facilitate termination. The structure of the post-termination complex shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The structure of the free Integrator-PP2A complex in an inactive closed conformation reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps that involve major rearrangements. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rc4.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8rc4.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 8rc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/8rc4 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/8rc4 | HTTPS FTP |
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-Related structure data
Related structure data | 19047MC 8rbxC 8rbzC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Serine/threonine-protein phosphatase 2A ... , 2 types, 2 molecules pq
#1: Protein | Mass: 65579.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30153 |
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#2: Protein | Mass: 35836.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P67775 |
-Protein/peptide , 1 types, 1 molecules r
#3: Protein/peptide | Mass: 3753.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper) |
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-Integrator complex subunit ... , 13 types, 13 molecules abdefghikmjno
#4: Protein | Mass: 244776.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N201 |
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#5: Protein | Mass: 134451.625 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS2, KIAA1287 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H0H0 |
#6: Protein | Mass: 108306.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS4, MSTP093 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96HW7 |
#7: Protein | Mass: 108316.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6P9B9 |
#8: Protein | Mass: 101166.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS6 / Production host: Trichoplusia (butterflies/moths) / References: UniProt: Q9UL03 |
#9: Protein | Mass: 107153.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVH2 |
#10: Protein | Mass: 113219.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS8, C8orf52 / Production host: Trichoplusia (butterflies/moths) / References: UniProt: Q75QN2 |
#11: Protein | Mass: 73891.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS9, RC74 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NV88 |
#12: Protein | Mass: 67956.750 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5TA45 |
#13: Protein | Mass: 80345.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS13, ASUN, C12orf11, GCT1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVM9 |
#14: Protein | Mass: 82339.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS10, C8orf35 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVR2 |
#15: Protein | Mass: 57526.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS14, C15orf44, VWA9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96SY0 |
#16: Protein | Mass: 50303.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: INTS15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96N11 |
-Non-polymers , 2 types, 4 molecules
#17: Chemical | #18: Chemical | |
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-Details
Has ligand of interest | Y |
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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 | Value: 1.5 MDa / Experimental value: NO | ||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) | ||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-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: OTHER |
Electron lens | Mode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 40.49 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement |
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CTF correction | Type: NONE |
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2335349 / Symmetry type: POINT |
Atomic model building | PDB-ID: 8RBX Accession code: 8RBX / Source name: PDB / Type: experimental model |