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: https://doi.org/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 RPB1A1,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2B1,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3C318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4D221Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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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 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
AMATOXINM8Amanita phalloidesMutation(s): 0 
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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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Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX		M L-PEPTIDE LINKINGC3 H7 N O3 SCYS
HYP
Query on HYP		M L-PEPTIDE LINKINGC5 H9 N O3PRO
ILX
Query on ILX		M L-PEPTIDE LINKINGC6 H13 N O4ILE
TRX
Query on TRX		M L-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

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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