+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19040 | ||||||||||||
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Title | Structure of Integrator-PP2A-SOSS-CTD post-termination 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 / SOSS complex / 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 ...regulation of fertilization / SOSS complex / 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 / establishment of protein localization to telomere / 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 / G-rich strand telomeric DNA binding / 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 / 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 / ERKs are inactivated / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / mitotic G2/M transition checkpoint / 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 / response to ionizing radiation / 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 / positive regulation of telomere capping / 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 / RNA polymerase II, core complex / DNA polymerase binding / regulation of cell adhesion Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Trichoplusia ni (cabbage looper) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 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_19040.map.gz | 245.8 MB | EMDB map data format | |
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Header (meta data) | emd-19040-v30.xml emd-19040.xml | 65.9 KB 65.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19040_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_19040.png | 45.5 KB | ||
Filedesc metadata | emd-19040.cif.gz | 16.5 KB | ||
Others | emd_19040_additional_1.map.gz emd_19040_additional_2.map.gz emd_19040_additional_3.map.gz emd_19040_additional_4.map.gz emd_19040_additional_5.map.gz emd_19040_additional_6.map.gz emd_19040_half_map_1.map.gz emd_19040_half_map_2.map.gz | 56.1 MB 55.7 MB 96.2 MB 56 MB 55 MB 55.9 MB 340.5 MB 340.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19040 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19040 | HTTPS FTP |
-Related structure data
Related structure data | 8rbzMC 8rbxC 8rc4C 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_19040.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
-Additional map: Focused refined map around Integrator cleavage module (INTS4,...
File | emd_19040_additional_1.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, INTS2 INTS7 and DSS1
File | emd_19040_additional_2.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 INTS5, INTS8 and INTS15
File | emd_19040_additional_3.map | ||||||||||||
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Annotation | Focused refined map around INTS5, INTS8 and INTS15 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around INTS6 and PP2A
File | emd_19040_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 INTS3 and SOSS factors
File | emd_19040_additional_5.map | ||||||||||||
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Annotation | Focused refined map around INTS3 and SOSS factors | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around INTS1 c-terminus and center of Integrator
File | emd_19040_additional_6.map | ||||||||||||
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Annotation | Focused refined map around INTS1 c-terminus and center of Integrator | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19040_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19040_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Post-termination complex
+Supramolecule #1: Post-termination complex
+Supramolecule #2: Integrator-PP2A complex and NABP2 and INIP
+Supramolecule #3: RNA Polymerase II C-terminal domain peptides
+Supramolecule #4: DSS1
+Macromolecule #1: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
+Macromolecule #2: SOSS complex subunit B1
+Macromolecule #3: SOSS complex subunit C
+Macromolecule #4: DNA-directed RNA polymerase subunit
+Macromolecule #5: Integrator complex subunit 1
+Macromolecule #6: Integrator complex subunit 2
+Macromolecule #7: Integrator complex subunit 3
+Macromolecule #8: Integrator complex subunit 4
+Macromolecule #9: Integrator complex subunit 5
+Macromolecule #10: Integrator complex subunit 6
+Macromolecule #11: Integrator complex subunit 7
+Macromolecule #12: Integrator complex subunit 8
+Macromolecule #13: Integrator complex subunit 9
+Macromolecule #14: Integrator complex subunit 10
+Macromolecule #15: Integrator complex subunit 11
+Macromolecule #16: Integrator complex subunit 14
+Macromolecule #17: Integrator complex subunit 15
+Macromolecule #18: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...
+Macromolecule #19: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...
+Macromolecule #20: DSS1
+Macromolecule #21: Integrator complex subunit 13
+Macromolecule #22: ZINC ION
+Macromolecule #23: MANGANESE (II) 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: 39.93 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Output model | PDB-8rbz: |