2VUM

Alpha-amanitin inhibited complete RNA polymerase II elongation complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation.

Brueckner, F.Cramer, P.

(2008) Nat Struct Mol Biol 15: 811

  • DOI: 10.1038/nsmb.1458
  • Primary Citation of Related Structures:  
    2VUM

  • PubMed Abstract: 
  • To study how RNA polymerase II translocates after nucleotide incorporation, we prepared elongation complex crystals in which pre- and post-translocation states interconvert. Crystal soaking with the inhibitor alpha-amanitin locked the elongation complex in a new state, which was refined at 3 ...

    To study how RNA polymerase II translocates after nucleotide incorporation, we prepared elongation complex crystals in which pre- and post-translocation states interconvert. Crystal soaking with the inhibitor alpha-amanitin locked the elongation complex in a new state, which was refined at 3.4-A resolution and identified as a possible translocation intermediate. The DNA base entering the active site occupies a 'pretemplating' position above the central bridge helix, which is shifted and occludes the templating position. A leucine residue in the trigger loop forms a wedge at the shifted bridge helix, but moves by 13 A to close the active site during nucleotide incorporation. Our results support a Brownian ratchet mechanism that involves swinging of the trigger loop between open, wedged and closed positions, and suggest that alpha-amanitin impairs nucleotide incorporation and translocation by trapping the trigger loop and bridge helix.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1A1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2B1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3C318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4D221Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1E215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2F155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7G171Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3H146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9I122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5J70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11K120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
AMATOXINM8Amanita phalloidesMutation(s): 0 
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  • Reference Sequence
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  • Entity ID: 14
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3'N14synthetic construct
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    • Entity ID: 15
      MoleculeChainsLengthOrganismImage
      5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'O [auth P]11synthetic construct
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      Entity ID: 16
      MoleculeChainsLengthOrganismImage
      5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *GP*TP*TP*AP*CP*GP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'P [auth T]26synthetic construct
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      • Reference Sequence
      Small Molecules
      Modified Residues  4 Unique
      IDChainsTypeFormula2D DiagramParent
      CSX
      Query on CSX
      ML-PEPTIDE LINKINGC3 H7 N O3 SCYS
      HYP
      Query on HYP
      ML-PEPTIDE LINKINGC5 H9 N O3PRO
      ILX
      Query on ILX
      ML-PEPTIDE LINKINGC6 H13 N O4ILE
      TRX
      Query on TRX
      ML-PEPTIDE LINKINGC11 H12 N2 O3TRP
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.40 Å
      • R-Value Free: 0.288 
      • R-Value Work: 0.255 
      • R-Value Observed: 0.255 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 220.619α = 90
      b = 394.234β = 90
      c = 283.966γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      XDSdata reduction
      XSCALEdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2008-06-17
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
      • Version 1.2: 2012-11-30
        Changes: Other
      • Version 1.3: 2018-06-27
        Changes: Data collection, Source and taxonomy, Structure summary