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 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1016/j.molcel.2008.04.023
  • Structures With Same Primary Citation

  • 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 ...

    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
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1A1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
ALPHA-AMANITINM8Amanita phalloidesMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2B1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3C318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1E215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2F155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3H146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9I122Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5J70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11K120Saccharomyces cerevisiaeMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000201
Query on PRD_000201
MAlpha-AmanitinC /  Toxin

--

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: 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 

  • 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