5M3M

Free monomeric RNA polymerase I at 4.0A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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

Structure of RNA polymerase I transcribing ribosomal DNA genes.

Neyer, S.Kunz, M.Geiss, C.Hantsche, M.Hodirnau, V.V.Seybert, A.Engel, C.Scheffer, M.P.Cramer, P.Frangakis, A.S.

(2016) Nature 540: 607-610

  • DOI: 10.1038/nature20561
  • Primary Citation of Related Structures:  
    5M3F, 5M3M

  • PubMed Abstract: 
  • RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation ...

    RNA polymerase I (Pol I) is a highly processive enzyme that transcribes ribosomal DNA (rDNA) and regulates growth of eukaryotic cells. Crystal structures of free Pol I from the yeast Saccharomyces cerevisiae have revealed dimers of the enzyme stabilized by a 'connector' element and an expanded cleft containing the active centre in an inactive conformation. The central bridge helix was unfolded and a Pol-I-specific 'expander' element occupied the DNA-template-binding site. The structure of Pol I in its active transcribing conformation has yet to be determined, whereas structures of Pol II and Pol III have been solved with bound DNA template and RNA transcript. Here we report structures of active transcribing Pol I from yeast solved by two different cryo-electron microscopy approaches. A single-particle structure at 3.8 Å resolution reveals a contracted active centre cleft with bound DNA and RNA, and a narrowed pore beneath the active site that no longer holds the RNA-cleavage-stimulating domain of subunit A12.2. A structure at 29 Å resolution that was determined from cryo-electron tomograms of Pol I enzymes transcribing cellular rDNA confirms contraction of the cleft and reveals that incoming and exiting rDNA enclose an angle of around 150°. The structures suggest a model for the regulation of transcription elongation in which contracted and expanded polymerase conformations are associated with active and inactive states, respectively.


    Organizational Affiliation

    Buchmann Institute for Molecular Life Sciences and Institute for Biophysics, Goethe University Frankfurt, Max-von-Laue Str. 15, Frankfurt 60438, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA190A1664Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA190RPA1RRN1YOR341WO6276
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA135B1203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA135RPA2RRN2SRP3YPR010CYP9531.03C
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1C335Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC40RPC5YPR110CP8283.18
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1D [auth E]215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2E [auth F]155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3F [auth H]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA12G [auth I]125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA12RRN4YJR063WJ1747
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5H [auth J]70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
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Entity ID: 9
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DNA-directed RNA polymerases I and III subunit RPAC2I [auth K]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC19YNL113WN1937
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4J [auth L]70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase I subunit RPA49K [auth M]415Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA49RRN13YNL248CN0880
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Entity ID: 12
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DNA-directed RNA polymerase I subunit RPA34L [auth N]233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA34YJL148WJ0637
UniProt
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Entity ID: 13
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DNA-directed RNA polymerase I subunit RPA14M [auth D]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA14YDR156WYD8358.11
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Entity ID: 14
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DNA-directed RNA polymerase I subunit RPA43N [auth G]326Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPA43RRN12YOR340CO6271
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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: 2016-11-23
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations