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Yorodumi- EMDB-19038: Structure of Integrator-PP2A bound to a paused RNA polymerase II-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19038 | ||||||||||||
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Title | Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex | ||||||||||||
Map data | Overall map filtered by local resolution | ||||||||||||
Sample |
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Keywords | Integrator complex / Pre-termination complex / TRANSCRIPTION | ||||||||||||
Function / homology | Function and homology information U2 snRNA 3'-end processing / regulation of fertilization / NELF complex / positive regulation of protein modification process / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation ...U2 snRNA 3'-end processing / regulation of fertilization / NELF complex / positive regulation of protein modification process / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / snRNA 3'-end processing / protein serine/threonine phosphatase complex / mitotic sister chromatid separation / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / snRNA processing / peptidyl-serine dephosphorylation / flagellated sperm motility / peptidyl-threonine dephosphorylation / FAR/SIN/STRIPAK complex / DSIF complex / protein localization to nuclear envelope / 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 phosphatase regulator activity / protein antigen binding / GABA receptor binding / integrator complex / regulation of transcription elongation by RNA polymerase II / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / 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 / Initiation of Nuclear Envelope (NE) Reformation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / negative regulation of stem cell differentiation / 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 / negative regulation of epithelial to mesenchymal transition / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / 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 / transcription elongation-coupled chromatin remodeling / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Platelet sensitization by LDL / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / protein-serine/threonine phosphatase / Cyclin A/B1/B2 associated events during G2/M transition / regulation of cell differentiation / RNA polymerase III activity / negative regulation of transcription elongation by RNA polymerase II / negative regulation of hippo signaling / ERK/MAPK targets / T cell homeostasis / regulation of mitotic cell cycle / regulation of G1/S transition of mitotic cell cycle / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / protein localization to CENP-A containing chromatin / mesoderm development Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Trichoplusia ni (cabbage looper) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 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_19038.map.gz | 229.1 MB | EMDB map data format | |
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Header (meta data) | emd-19038-v30.xml emd-19038.xml | 96.3 KB 96.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19038_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_19038.png | 50.5 KB | ||
Masks | emd_19038_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-19038.cif.gz | 22.6 KB | ||
Others | emd_19038_additional_1.map.gz emd_19038_additional_2.map.gz emd_19038_additional_3.map.gz emd_19038_additional_4.map.gz emd_19038_additional_5.map.gz emd_19038_additional_6.map.gz emd_19038_half_map_1.map.gz emd_19038_half_map_2.map.gz | 161.4 MB 93.8 MB 92.6 MB 54.3 MB 93.9 MB 92.3 MB 383.7 MB 383.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19038 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19038 | HTTPS FTP |
-Related structure data
Related structure data | 8rbxMC 8rbzC 8rc4C M: atomic model generated by this map C: citing same article (ref.) |
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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_19038.map.gz / Format: CCP4 / Size: 476.8 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_19038_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around Pol II, DSIF, NELF and nucleic acids
File | emd_19038_additional_1.map | ||||||||||||
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Annotation | Focused refined map around Pol II, DSIF, NELF and nucleic acids | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around INTS5, INTS6, INTS8 and PP2A
File | emd_19038_additional_2.map | ||||||||||||
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Annotation | Focused refined map around INTS5, INTS6, INTS8 and PP2A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Focused refined map around PP2A
File | emd_19038_additional_3.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 cleavage module (INTS4,...
File | emd_19038_additional_4.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_19038_additional_5.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 tail module (INTS10,...
File | emd_19038_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_19038_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19038_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Pre-termination complex
+Supramolecule #1: Pre-termination complex
+Supramolecule #2: Integrator-PP2A complex and NELF
+Supramolecule #3: Nucleosome
+Supramolecule #5: RNA and DNA
+Supramolecule #4: DNA-directed RNA Polymerase II
+Supramolecule #6: DSIF
+Macromolecule #1: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
+Macromolecule #2: DNA-directed RNA polymerase subunit
+Macromolecule #3: DNA-directed RNA polymerase subunit beta
+Macromolecule #4: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #5: RNA polymerase II subunit D
+Macromolecule #6: DNA-directed RNA polymerase II subunit E
+Macromolecule #7: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #8: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #9: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #10: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #12: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #13: RNA polymerase II subunit K
+Macromolecule #14: Histone H3.3C
+Macromolecule #16: Histone H4
+Macromolecule #18: Histone H2A type 1
+Macromolecule #19: Histone H2B type 1-J
+Macromolecule #21: Transcription elongation factor SPT5
+Macromolecule #22: Integrator complex subunit 1
+Macromolecule #23: Integrator complex subunit 2
+Macromolecule #24: Integrator complex subunit 4
+Macromolecule #25: Integrator complex subunit 5
+Macromolecule #26: Integrator complex subunit 6
+Macromolecule #27: Integrator complex subunit 7
+Macromolecule #28: Integrator complex subunit 8
+Macromolecule #29: Integrator complex subunit 9
+Macromolecule #30: Integrator complex subunit 10
+Macromolecule #31: Integrator complex subunit 11
+Macromolecule #32: Integrator complex subunit 13
+Macromolecule #33: Integrator complex subunit 14
+Macromolecule #34: Integrator complex subunit 15
+Macromolecule #35: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...
+Macromolecule #36: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...
+Macromolecule #37: DSS1
+Macromolecule #38: Negative elongation factor A
+Macromolecule #39: NELF-B,Negative elongation factor B,Negative elongation factor B,...
+Macromolecule #40: Negative elongation factor C/D
+Macromolecule #41: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-U...
+Macromolecule #15: non-template DNA
+Macromolecule #20: Template DNA
+Macromolecule #17: RNA
+Macromolecule #42: ZINC ION
+Macromolecule #43: MAGNESIUM ION
+Macromolecule #44: 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 |
Grid | Model: Qu / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.44 e/Å2 |
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 |
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-8rbx: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Output model | PDB-8rbx: |
-Atomic model buiding 3
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Output model | PDB-8rbx: |
-Atomic model buiding 4
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | PDB-8rbx: |