5W5Y

RNA polymerase I Initial Transcribing Complex

  • Classification: TRANSCRIPTION
  • Organism(s): Saccharomyces cerevisiae S288C
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-06-16 Released: 2017-07-26 
  • Deposition Author(s): Han, Y., He, Y.
  • Funding Organization(s): Northwestern University, American Cancer Society, National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.

Han, Y., Yan, C., Nguyen, T.H.D., Jackobel, A.J., Ivanov, I., Knutson, B.A., He, Y.

(2017) Elife 6

  • DOI: https://doi.org/10.7554/eLife.27414
  • Primary Citation of Related Structures:  
    5W5Y, 5W64, 5W65, 5W66

  • PubMed 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 structure of Saccharomyces cerevisiae 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.

    • Organizational Affiliation: 

    Department of Molecular Biosciences, Northwestern University, Evanston, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA1901,664Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA1351,203Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P22138 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1335Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA14137Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA43326Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA12125Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC2142Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA49415Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA34233Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN6894Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN6, YBL014C, YBL0311, YBL0312
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN7514Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN7, YJL025W, J1273
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN11507Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN11, YML043C, YM9827.09C
UniProt
Find proteins for Q04712 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChains LengthOrganismImage
RNA6Saccharomyces cerevisiae S288C
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Entity ID: 19
MoleculeChains LengthOrganismImage
non-template strand DNA54Saccharomyces cerevisiae S288C
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Entity ID: 20
MoleculeChains LengthOrganismImage
template strand DNA54Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot0.8.8
MODEL REFINEMENTPHENIX1.10.1
RECONSTRUCTIONRELION2.0

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2017-07-26 
    • Deposition Author(s): Han, Y., He, Y.
Funding OrganizationLocationGrant Number
Northwestern UniversityUnited StatesCornew Innovation Award
American Cancer SocietyUnited StatesIRG-15-173-21
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesNCI 5K22CA184235
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesNIGMS GM110387
National Science Foundation (NSF, United States)United StatesMCB-1149521

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2017-11-08
    Changes: Derived calculations
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.5: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary