1K83

Crystal Structure of Yeast RNA Polymerase II Complexed with the Inhibitor Alpha Amanitin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structural Basis of Transcription: Alpha-Amanitin-RNA Polymerase II Cocrystal at 2.8 A Resolution.

Bushnell, D.A., Cramer, P., Kornberg, R.D.

(2002) Proc Natl Acad Sci U S A 99: 1218

  • DOI: 10.1073/pnas.251664698
  • Primary Citation of Related Structures:  
    1K83

  • PubMed Abstract: 

    • The structure of RNA polymerase II in a complex with the inhibitor alpha-amanitin has been determined by x-ray crystallography. The structure of the complex indicates the likely basis of inhibition and gives unexpected insight into the transcription mechanism ...

    The structure of RNA polymerase II in a complex with the inhibitor alpha-amanitin has been determined by x-ray crystallography. The structure of the complex indicates the likely basis of inhibition and gives unexpected insight into the transcription mechanism.

    Organizational Affiliation: 

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNITA1,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDEB1,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDEC318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 27KD POLYPEPTIDED [auth E]215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 23KD POLYPEPTIDEE [auth F]155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 14.5KD POLYPEPTIDEF [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDEG [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 8.3KD POLYPEPTIDEH [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDEI [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 7.7KD POLYPEPTIDEJ [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA AMANITINK [auth M]8Amanita phalloidesMutation(s): 0 
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UniProt GroupP85421
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Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX		K [auth M]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
HYP
Query on HYP		K [auth M]L-PEPTIDE LINKINGC5 H9 N O3PRO
ILX
Query on ILX		K [auth M]L-PEPTIDE LINKINGC6 H13 N O4ILE
TRX
Query on TRX		K [auth M]L-PEPTIDE LINKINGC11 H12 N2 O3TRP
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 11
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000201
Query on PRD_000201		K [auth M]Alpha-AmanitinCyclic peptide / Toxin Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • 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
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-13
    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: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other