5OA1

RNA polymerase I pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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 insights into transcription initiation by yeast RNA polymerase I.

Sadian, Y.Tafur, L.Kosinski, J.Jakobi, A.J.Wetzel, R.Buczak, K.Hagen, W.J.Beck, M.Sachse, C.Muller, C.W.

(2017) EMBO J 36: 2698-2709

  • DOI: https://doi.org/10.15252/embj.201796958
  • Primary Citation of Related Structures:  
    5OA1

  • PubMed Abstract: 

    In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo-EM structure of the 18-subunit yeast Pol I PIC bound to a transcription scaffold. The cryo-EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB-related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.


  • Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, 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
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
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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 
UniProt
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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 
UniProt
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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 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN3627Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN7R [auth U]514Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN7YJL025WJ1273
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN6S [auth V]894Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN6YBL014CYBL0311YBL0312
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase I-specific transcription initiation factor RRN11T [auth W]507Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRN11YML043CYM9827.09C
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAU [auth 1]13Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAV [auth 2]19Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALACA [auth 9],
W [auth 3]
9Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAX [auth 4]24Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALADA [auth Q],
Y [auth 5]
16Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALABA [auth 8],
Z [auth 6]
10Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAAA [auth 7]25Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAEA [auth P]22Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAFA [auth Z]15Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAGA [auth Y]12Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALA-ALAHA [auth R]27Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA (49-MER)P [auth S]70Saccharomyces cerevisiae S288C
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Entity ID: 17
MoleculeChains LengthOrganismImage
DNA (56-MER)Q [auth T]70Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-26
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Database references
  • Version 1.2: 2017-12-06
    Changes: Advisory, Database references
  • Version 1.3: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations