3CQZ

Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

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This is version 1.5 of the entry. See complete history


Literature

The RNA Polymerase II Trigger Loop Functions in Substrate Selection and is Directly Targeted by Alpha-Amanitin.

Kaplan, C.D.Larsson, K.M.Kornberg, R.D.

(2008) Mol Cell 30: 547

  • DOI: https://doi.org/10.1016/j.molcel.2008.04.023
  • Primary Citation of Related Structures:  
    3CQZ

  • PubMed Abstract: 

    Structural, biochemical, and genetic studies have led to proposals that a mobile element of multisubunit RNA polymerases, the Trigger Loop (TL), plays a critical role in catalysis and can be targeted by antibiotic inhibitors. Here we present evidence that the Saccharomyces cerevisiae RNA Polymerase II (Pol II) TL participates in substrate selection. Amino acid substitutions within the Pol II TL preferentially alter substrate usage and enzyme fidelity, as does inhibition of transcription by alpha-amanitin. Finally, substitution of His1085 in the TL specifically renders Pol II highly resistant to alpha-amanitin, indicating a functional interaction between His1085 and alpha-amanitin that is supported by rerefinement of an alpha-amanitin-Pol II crystal structure. We propose that alpha-amanitin-inhibited Pol II elongation, which is slow and exhibits reduced substrate selectivity, results from direct alpha-amanitin interference with the TL.


  • Organizational Affiliation

    Department of Structural Biology, Stanford University, Stanford, CA 94305, USA. cdkaplan@stanford.edu


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB21,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1D [auth E]215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2E [auth F]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3F [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9G [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5H [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11I [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4J [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-AMANITINK [auth M]8Amanita phalloidesMutation(s): 0 
UniProt
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UniProt GroupP85421
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Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.51α = 90
b = 222.48β = 90
c = 374.23γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description