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- EMDB-36908: Cryo-EM structure of yeast Rat1-bound Pol II pre-termination tran... -
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Open data
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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 / ![]() ![]() | |||||||||
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 / phosphodiesterase decapping endonuclease activity / termination of RNA polymerase II transcription, poly(A)-coupled ...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 / phosphodiesterase decapping endonuclease activity / 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 / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / 5'-3' RNA exonuclease activity / regulation of rRNA processing / RNA polymerase I core binding / intracellular mRNA localization / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
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Method | ![]() ![]() | |||||||||
![]() | Zeng Y / Zhang Y | |||||||||
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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 |
-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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-Half map: #2
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-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 | ![]() |
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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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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 |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |