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Open data
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Basic information
Entry | Database: PDB / ID: 5w5y | ||||||||||||||||||
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Title | RNA polymerase I Initial Transcribing Complex | ||||||||||||||||||
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Function / homology | ![]() RNA polymerase I core factor complex / RNA polymerase transcription factor SL1 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 I core factor complex / RNA polymerase transcription factor SL1 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 | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmcif format | ![]() ![]() ![]() |
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PDB format | ![]() ![]() |
PDBML Plus | ![]() |
Others | ![]() |
-Related structure data
Related structure data | ![]() 8771CM ![]() 8772C ![]() 8773C ![]() 8774C ![]() 8775C ![]() 8776C ![]() 8777C ![]() 5w64C ![]() 5w65C ![]() 5w66C C: citing same article ( M: map data used to model this data |
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Similar-shape strucutres |
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Links
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Assembly
Deposited unit | ![]()
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Components
+DNA-directed RNA polymerase I subunit ... , 7 types, 7 molecules ABDGIMN
+DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK
+DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
+RNA polymerase I-specific transcription initiation factor ... , 3 types, 3 molecules OPQ
+DNA chain , 2 types, 2 molecules ST
+RNA chain / Non-polymers , 2 types, 7 molecules R

+Details
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: RNA Polymerase I Initial Transcribing Complex / Type: COMPLEX / Entity ID: #1-#20 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.9 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() |
Specimen support | Grid material: ![]() |
Vitrification![]() | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 12 sec. / Electron dose: 56.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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CTF correction![]() | Details: CTF amplitude correction was performed following 3D auto refinement in relion. Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124112 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |