+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19047 | ||||||||||||
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Title | Structure of Integrator-PP2A complex | ||||||||||||
Map data | Overall map filtered by local resolution | ||||||||||||
Sample |
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Keywords | Integrator complex / Post-termination complex / RNA Polymerase II / Pol II / RNAPII / TRANSCRIPTION | ||||||||||||
Function / homology | Function and homology information regulation of fertilization / U2 snRNA 3'-end processing / snRNA processing / integrator complex / intercellular transport / snRNA 3'-end processing / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding ...regulation of fertilization / U2 snRNA 3'-end processing / snRNA processing / integrator complex / intercellular transport / 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 / meiotic sister chromatid cohesion, centromeric / flagellated sperm motility / peptidyl-serine dephosphorylation / : / protein localization to nuclear envelope / regulation of transcription elongation by RNA polymerase II / peptidyl-threonine dephosphorylation / negative regulation of tyrosine phosphorylation of STAT protein / positive regulation of microtubule binding / 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 / ceramide metabolic process / protein phosphatase regulator activity / 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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / 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 / regulation of Wnt signaling pathway / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / 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 / phosphoprotein phosphatase activity / regulation of DNA replication / mesoderm development / RNA polymerase II transcribes snRNA genes / chromosome, centromeric region / DARPP-32 events / lateral plasma membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / regulation of mitotic cell cycle / Anchoring of the basal body to the plasma membrane / 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 / cellular response to ionizing radiation / RHO GTPases Activate Formins / 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 Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Trichoplusia ni (cabbage looper) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Fianu I / Ochmann M / Walshe JL / Cramer P | ||||||||||||
Funding support | Germany, European Union, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19047.map.gz | 208.3 MB | EMDB map data format | |
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Header (meta data) | emd-19047-v30.xml emd-19047.xml | 58.6 KB 58.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19047_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_19047.png | 37.2 KB | ||
Masks | emd_19047_msk_1.map | 421.9 MB | Mask map | |
Filedesc metadata | emd-19047.cif.gz | 15.4 KB | ||
Others | emd_19047_additional_1.map.gz emd_19047_additional_2.map.gz emd_19047_additional_3.map.gz emd_19047_additional_4.map.gz emd_19047_additional_5.map.gz emd_19047_additional_6.map.gz emd_19047_half_map_1.map.gz emd_19047_half_map_2.map.gz | 54.8 MB 54.9 MB 153.2 MB 55.2 MB 55.2 MB 95.7 MB 338.5 MB 338.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19047 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19047 | HTTPS FTP |
-Related structure data
Related structure data | 8rc4MC 8rbxC 8rbzC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19047.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Overall map filtered by local resolution | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19047_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around INTS1, INTS2 INTS7 and DSS1
File | emd_19047_additional_1.map | ||||||||||||
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Annotation | Focused refined map around INTS1, INTS2 INTS7 and DSS1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around Integrator cleavage module (INTS4,...
File | emd_19047_additional_2.map | ||||||||||||
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Annotation | Focused refined map around Integrator cleavage module (INTS4, INTS9 and INTS11) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around INTS1 c-terminus and central...
File | emd_19047_additional_3.map | ||||||||||||
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Annotation | Focused refined map around INTS1 c-terminus and central core of Integrator | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around INTS6 and PP2A
File | emd_19047_additional_4.map | ||||||||||||
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Annotation | Focused refined map around INTS6 and PP2A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around PP2A
File | emd_19047_additional_5.map | ||||||||||||
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Annotation | Focused refined map around PP2A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around Integrator tail module (INTS10,...
File | emd_19047_additional_6.map | ||||||||||||
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Annotation | Focused refined map around Integrator tail module (INTS10, INTS13 , INTS14 and INTS15) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19047_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19047_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Integrator-PP2A complex
+Supramolecule #1: Integrator-PP2A complex
+Supramolecule #2: Integrator-PP2A complex
+Supramolecule #3: DSS1
+Macromolecule #1: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...
+Macromolecule #2: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...
+Macromolecule #3: DSS1
+Macromolecule #4: Integrator complex subunit 1
+Macromolecule #5: Integrator complex subunit 2
+Macromolecule #6: Integrator complex subunit 4
+Macromolecule #7: Integrator complex subunit 5
+Macromolecule #8: Integrator complex subunit 6
+Macromolecule #9: Integrator complex subunit 7
+Macromolecule #10: Integrator complex subunit 8
+Macromolecule #11: Integrator complex subunit 9
+Macromolecule #12: Integrator complex subunit 11
+Macromolecule #13: Integrator complex subunit 13
+Macromolecule #14: Integrator complex subunit 10
+Macromolecule #15: Integrator complex subunit 14
+Macromolecule #16: Integrator complex subunit 15
+Macromolecule #17: MANGANESE (II) ION
+Macromolecule #18: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-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: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.49 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |