1R9T

RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.239 

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This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.

Westover, K.D., Bushnell, D.A., Kornberg, R.D.

(2004) Cell 119: 481-489

  • DOI: 10.1016/j.cell.2004.10.016
  • Primary Citation of Related Structures:  
    1R9S, 1R9T, 1TWA, 1TWC, 1TWF, 1TWG, 1TWH

  • PubMed Abstract: 

    • Binding of a ribonucleoside triphosphate to an RNA polymerase II transcribing complex, with base pairing to the template DNA, was revealed by X-ray crystallography. Binding of a mismatched nucleoside triphosphate was also detected, but in an adjacent site, inverted with respect to the correctly paired nucleotide ...

    Binding of a ribonucleoside triphosphate to an RNA polymerase II transcribing complex, with base pairing to the template DNA, was revealed by X-ray crystallography. Binding of a mismatched nucleoside triphosphate was also detected, but in an adjacent site, inverted with respect to the correctly paired nucleotide. The results are consistent with a two-step mechanism of nucleotide selection, with initial binding to an entry (E) site beneath the active center in an inverted orientation, followed by rotation into the nucleotide addition (A) site for pairing with the template DNA. This mechanism is unrelated to that of single subunit RNA polymerases and so defines a new paradigm for the large, multisubunit enzymes. Additional findings from these studies include a third nucleotide binding site that may define the length of backtracked RNA; DNA double helix unwinding in advance of the polymerase active center; and extension of the diffraction limit of RNA polymerase II crystals to 2.3 A.

    Organizational Affiliation: 

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



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II largest subunitD [auth A]1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 140 kDa polypeptideE [auth B]1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 45 kDa polypeptideF [auth C]318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptideG [auth E]215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptideH [auth F]155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptideI [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 14.2 kDa polypeptideJ [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptideK [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 13.6 kDa polypeptideL [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptideM [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA strandA [auth R]10N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA template strandB [auth T]28N/A
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA nontemplate strandC [auth N]14N/A
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.846α = 90
b = 222.958β = 101.17
c = 193.602γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-16
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance