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- EMDB-8777: Pol I Initial Transcribing Complex with a truncated scaffold at 6... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8777 | ||||||||||||||||||
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Title | Pol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom | ||||||||||||||||||
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![]() | RNA Polymerase I Initial Transcribing Complex with a truncated scaffold
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Function / homology | ![]() RNA polymerase transcription factor SL1 complex / RNA polymerase I core factor complex / RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase I preinitiation complex assembly / nucleolar large rRNA transcription by RNA polymerase I / transposon integration ...RNA polymerase transcription factor SL1 complex / RNA polymerase I core factor complex / RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase I preinitiation complex assembly / nucleolar large rRNA transcription by RNA polymerase I / transposon integration / transcription elongation from RNA polymerase I promoter / termination of RNA polymerase I transcription / termination of RNA polymerase III transcription / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||
![]() | Han Y / He Y | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. Authors: Yan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He / ![]() Abstract: Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a ...Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC. | ||||||||||||||||||
Validation Report | ![]() ![]() ![]() ![]() | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
FSC (resolution estimation) |
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Header (meta data in XML format) |
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Images |
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Archive directory |
-Related structure data
Related structure data | ![]() 8771C ![]() 8772C ![]() 8773C ![]() 8774C ![]() 8775C ![]() 8776C ![]() 5w5yC ![]() 5w64C ![]() 5w65C ![]() 5w66C C: citing same article ( |
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Similar-shape strucutres |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.36 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire RNA Polymerase I Initial Transcribing Complex with a truncated sc...
+Component #1: protein, RNA Polymerase I Initial Transcribing Complex with a tru...
+Component #2: protein, DNA-directed RNA polymerase I subunit RPA190
+Component #3: protein, DNA-directed RNA polymerase I subunit RPA135
+Component #4: protein, DNA-directed RNA polymerases I and III subunit RPAC1
+Component #5: protein, DNA-directed RNA polymerase I subunit RPA14
+Component #6: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1
+Component #7: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Component #8: protein, DNA-directed RNA polymerase I subunit RPA43
+Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Component #10: protein, DNA-directed RNA polymerase I subunit RPA12
+Component #11: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Component #12: protein, DNA-directed RNA polymerases I and III subunit RPAC2
+Component #13: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Component #14: protein, DNA-directed RNA polymerase I subunit RPA49
+Component #15: protein, DNA-directed RNA polymerase I subunit RPA34
+Component #16: protein, RNA polymerase I-specific transcription initiation facto...
+Component #17: protein, RNA polymerase I-specific transcription initiation facto...
+Component #18: protein, RNA polymerase I-specific transcription initiation facto...
+Component #19: nucleic-acid, RNA
+Component #20: nucleic-acid, template strand DNA
+Component #21: nucleic-acid, upstream non-template strand DNA
+Component #22: nucleic-acid, downstream non-template strand DNA
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Sample solution | pH: 7.6 |
Vitrification | Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 % |
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Electron microscopy imaging
![]() | Microscope: JEOL 3200FS |
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Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 15000.0 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Model: GATAN LIQUID NITROGEN |
Camera | Detector: GATAN K2 SUMMIT (4k x 4k) |
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Image processing
-Atomic model buiding
Modeling #1 | Refinement protocol: flexible / Refinement space: REAL |
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