[English] 日本語
![](img/lk-miru.gif)
- EMDB-10006: RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 -
+
Open data
-
Basic information
Entry | Database: EMDB / ID: EMD-10006 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 | |||||||||
![]() | RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 | |||||||||
![]() |
| |||||||||
![]() | ![]() ![]() ![]() ![]() | |||||||||
Function / homology | ![]() RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I core factor complex / RNA polymerase I core binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Mueller CW / Sadian Y | |||||||||
Funding support | 1 items
| |||||||||
![]() | ![]() Title: Molecular insight into RNA polymerase I promoter recognition and promoter melting. Authors: Yashar Sadian / Florence Baudin / Lucas Tafur / Brice Murciano / Rene Wetzel / Felix Weis / Christoph W Müller / ![]() ![]() Abstract: RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I ...RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I initiation complexes from 2.7 to 3.7 Å resolution to visualize Pol I promoter melting and to structurally and biochemically characterize the recognition mechanism of Pol I promoter DNA. In the closed complex, double-stranded DNA runs outside the DNA-binding cleft. Rotation of CF and upstream DNA with respect to Pol I and Rrn3 results in the spontaneous loading and opening of the promoter followed by cleft closure and positioning of the Pol I A49 tandem winged helix domain (tWH) onto DNA. Conformational rearrangement of A49 tWH leads to a clash with Rrn3 to initiate complex disassembly and promoter escape. Comprehensive insight into the Pol I transcription initiation cycle allows comparisons with promoter opening by Pol II and Pol III. | |||||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
-
Downloads & links
-EMDB archive
Map data | ![]() | 16.7 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 41 KB 41 KB | Display Display | ![]() |
Images | ![]() | 65 KB | ||
Filedesc metadata | ![]() | 11.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ruiMC ![]() 4982C ![]() 4984C ![]() 4985C ![]() 4987C ![]() 6rqhC ![]() 6rqlC ![]() 6rqtC ![]() 6rrdC ![]() 6ruoC ![]() 6rweC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | RNA Polymerase I Pre-initiation complex DNA opening intermediate 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-
Sample components
+Entire : RNA Polymerase I Pre-initiation complex DNA opening intermediate 2
+Supramolecule #1: RNA Polymerase I Pre-initiation complex DNA opening intermediate 2
+Supramolecule #2: RNA Polymerase I
+Supramolecule #3: DNA
+Supramolecule #4: transcription initiation factors
+Macromolecule #1: Template strand
+Macromolecule #2: Nontemplate strand
+Macromolecule #3: DNA-directed RNA polymerase I subunit RPA12
+Macromolecule #4: DNA-directed RNA polymerase I subunit RPA34
+Macromolecule #5: DNA-directed RNA polymerase I subunit RPA49
+Macromolecule #6: DNA-directed RNA polymerase I subunit RPA190
+Macromolecule #7: DNA-directed RNA polymerase I subunit RPA135
+Macromolecule #8: DNA-directed RNA polymerases I and III subunit RPAC1
+Macromolecule #9: DNA-directed RNA polymerase I subunit RPA14
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Macromolecule #11: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #12: DNA-directed RNA polymerase I subunit RPA43
+Macromolecule #13: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #14: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #15: DNA-directed RNA polymerases I and III subunit RPAC2
+Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #17: RNA polymerase I-specific transcription initiation factor RRN3
+Macromolecule #18: RNA polymerase I-specific transcription initiation factor RRN7
+Macromolecule #19: RNA polymerase I-specific transcription initiation factor RRN6
+Macromolecule #20: RNA polymerase I-specific transcription initiation factor RRN11
+Macromolecule #21: ZINC ION
-Experimental details
-Structure determination
Method | ![]() |
---|---|
![]() | ![]() |
Aggregation state | particle |
-
Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.1075 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Startup model | Type of model: EMDB MAP |
---|---|
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42727 |