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- EMDB-36908: Cryo-EM structure of yeast Rat1-bound Pol II pre-termination tran... -
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Basic information
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Title | Cryo-EM structure of yeast Rat1-bound Pol II pre-termination transcription complex 2 (Pol II Rat1-PTTC2) | |||||||||
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![]() | Transcription termination / Pol II / Rat1/Rai1 Spt5 / TRANSCRIPTION | |||||||||
Function / homology | ![]() RNA polymerase II termination complex / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / positive regulation of transcription elongation by RNA polymerase I / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / regulation of transcription-coupled nucleotide-excision repair / termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent ...RNA polymerase II termination complex / negative regulation of transcription elongation by RNA polymerase I / sno(s)RNA processing / positive regulation of termination of RNA polymerase II transcription / positive regulation of transcription elongation by RNA polymerase I / RNA NAD+-cap (NAD+-forming) hydrolase activity / Las1 complex / regulation of transcription-coupled nucleotide-excision repair / termination of RNA polymerase II transcription, poly(A)-coupled / termination of RNA polymerase II transcription, exosome-dependent / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / snRNP binding / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / 5'-3' RNA exonuclease activity / mRNA 5'-diphosphatase activity / regulation of rRNA processing / RNA polymerase I core binding / DSIF complex / nucleic acid metabolic process / intracellular mRNA localization / nuclear mRNA surveillance / RNA polymerase I general transcription initiation factor binding / RPB4-RPB7 complex / U4 snRNA binding / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / nuclear-transcribed mRNA catabolic process / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription elongation-coupled chromatin remodeling / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase II transcription / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / : / Formation of TC-NER Pre-Incision Complex / : / termination of RNA polymerase I transcription / spliceosomal complex assembly / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / negative regulation of transcription elongation by RNA polymerase II / RNA polymerase II complex binding / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / transcription by RNA polymerase III / Dual incision in TC-NER / transcription elongation by RNA polymerase I / U5 snRNA binding / positive regulation of translational initiation / RNA polymerase I complex / RNA polymerase III complex / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / U2 snRNA binding / U6 snRNA binding / tRNA transcription by RNA polymerase III / positive regulation of autophagy / RNA polymerase I activity / translesion synthesis / RNA polymerase II activity / enzyme regulator activity / U1 snRNA binding / translation initiation factor binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-templated transcription initiation / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / mRNA processing / DNA-directed 5'-3' RNA polymerase activity / cytoplasmic stress granule / DNA-directed RNA polymerase / rRNA processing / peroxisome / ribosome biogenesis Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
![]() | Zeng Y / Zhang Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of exoribonuclease-mediated mRNA transcription termination. Authors: Yuan Zeng / Hong-Wei Zhang / Xiao-Xian Wu / Yu Zhang / ![]() Abstract: Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II ...Efficient termination is required for robust gene transcription. Eukaryotic organisms use a conserved exoribonuclease-mediated mechanism to terminate the mRNA transcription by RNA polymerase II (Pol II). Here we report two cryogenic electron microscopy structures of Saccharomyces cerevisiae Pol II pre-termination transcription complexes bound to the 5'-to-3' exoribonuclease Rat1 and its partner Rai1. Our structures show that Rat1 displaces the elongation factor Spt5 to dock at the Pol II stalk domain. Rat1 shields the RNA exit channel of Pol II, guides the nascent RNA towards its active centre and stacks three nucleotides at the 5' terminus of the nascent RNA. The structures further show that Rat1 rotates towards Pol II as it shortens RNA. Our results provide the structural mechanism for the Rat1-mediated termination of mRNA transcription by Pol II in yeast and the exoribonuclease-mediated termination of mRNA transcription in other eukaryotes. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 123.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 39 KB 39 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.1 KB | Display | ![]() |
Images | ![]() | 127.2 KB | ||
Filedesc metadata | ![]() | 11.4 KB | ||
Others | ![]() ![]() ![]() | 117.3 MB 226.3 MB 226.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 855.9 KB | Display | ![]() |
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Full document | ![]() | 855.4 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 27.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k5pMC ![]() 8jchC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : RNA Polymerase II pre-termination complex bound with Rat1-Rai1 an...
+Supramolecule #1: RNA Polymerase II pre-termination complex bound with Rat1-Rai1 an...
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #5: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #6: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB11
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #14: Transcription elongation factor SPT5
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #16: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #17: 5'-3' exoribonuclease 2
+Macromolecule #18: Decapping nuclease RAI1
+Macromolecule #11: DNA (38-MER)
+Macromolecule #13: DNA (38-MER)
+Macromolecule #12: RNA
+Macromolecule #19: ZINC ION
+Macromolecule #20: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 0.01 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |