5N60

Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation I)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of RNA Polymerase I Transcription Initiation.

Engel, C.Gubbey, T.Neyer, S.Sainsbury, S.Oberthuer, C.Baejen, C.Bernecky, C.Cramer, P.

(2017) Cell 169: 120-131.e22

  • DOI: https://doi.org/10.1016/j.cell.2017.03.003
  • Primary Citation of Related Structures:  
    5N5Y, 5N5Z, 5N60, 5N61, 5O7X

  • PubMed Abstract: 

    Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct "bendability" and "meltability" of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.


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
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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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1335Saccharomyces cerevisiae S288CMutation(s): 0 
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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
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA43326Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA12125Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
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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 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA34233Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN3627Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN3YKL125W
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN6894Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN6YBL014CYBL0311YBL0312
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN7514Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN7YJL025WJ1273
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN11507Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN11YML043CYM9827.09C
UniProt
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB860, SPP1935
The Advanced Grant TRANSREGULON from the European Research CouncilGermany693023
Volkswagen FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Structure summary
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2018-10-03
    Changes: Advisory, Data collection, Derived calculations