4C2M

Structure of RNA polymerase I at 2.8 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

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This is version 1.2 of the entry. See complete history


Literature

RNA Polymerase I Structure and Transcription Regulation.

Engel, C.Sainsbury, S.Cheung, A.C.Kostrewa, D.Cramer, P.

(2013) Nature 502: 502

  • DOI: 10.1038/nature12712
  • Primary Citation of Related Structures:  
    4C2M

  • PubMed Abstract: 
  • Transcription of ribosomal RNA by RNA polymerase (Pol) I initiates ribosome biogenesis and regulates eukaryotic cell growth. The crystal structure of Pol I from the yeast Saccharomyces cerevisiae at 2.8 Å resolution reveals all 14 subunits of the 590-kil ...

    Transcription of ribosomal RNA by RNA polymerase (Pol) I initiates ribosome biogenesis and regulates eukaryotic cell growth. The crystal structure of Pol I from the yeast Saccharomyces cerevisiae at 2.8 Å resolution reveals all 14 subunits of the 590-kilodalton enzyme, and shows differences to Pol II. An 'expander' element occupies the DNA template site and stabilizes an expanded active centre cleft with an unwound bridge helix. A 'connector' element invades the cleft of an adjacent polymerase and stabilizes an inactive polymerase dimer. The connector and expander must detach during Pol I activation to enable transcription initiation and cleft contraction by convergent movement of the polymerase 'core' and 'shelf' modules. Conversion between an inactive expanded and an active contracted polymerase state may generally underlie transcription. Regulatory factors can modulate the core-shelf interface that includes a 'composite' active site for RNA chain initiation, elongation, proofreading and termination.


    Organizational Affiliation

    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4 1L70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA49 2M415Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q01080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA34 3N233Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P47006 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA43 4GOV326Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P46669 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA190 AP1664Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P10964 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA135 BQ1203Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P22138 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC1 CR335Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA14 DS137Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 ET215Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2 FU155Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3 HW146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE I SUBUNIT RPA12 IX125Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P32529 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5 JY70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I AND III SUBUNIT RPAC2 KZ142Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.74α = 108.06
b = 139.02β = 95.4
c = 209.55γ = 93.85
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
autoSHARPphasing
PARROTphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2013-11-06
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Derived calculations