3PO3

Arrested RNA Polymerase II reactivation intermediate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of RNA polymerase II backtracking, arrest and reactivation.

Cheung, A.C.Cramer, P.

(2011) Nature 471: 249-253

  • DOI: 10.1038/nature09785
  • Primary Citation of Related Structures:  
    3PO2, 3PO3

  • PubMed Abstract: 
  • During gene transcription, RNA polymerase (Pol) II moves forwards along DNA and synthesizes messenger RNA. However, at certain DNA sequences, Pol II moves backwards, and such backtracking can arrest transcription. Arrested Pol II is reactivated by transcription factor IIS (TFIIS), which induces RNA cleavage that is required for cell viability ...

    During gene transcription, RNA polymerase (Pol) II moves forwards along DNA and synthesizes messenger RNA. However, at certain DNA sequences, Pol II moves backwards, and such backtracking can arrest transcription. Arrested Pol II is reactivated by transcription factor IIS (TFIIS), which induces RNA cleavage that is required for cell viability. Pol II arrest and reactivation are involved in transcription through nucleosomes and in promoter-proximal gene regulation. Here we present X-ray structures at 3.3 Å resolution of an arrested Saccharomyces cerevisiae Pol II complex with DNA and RNA, and of a reactivation intermediate that additionally contains TFIIS. In the arrested complex, eight nucleotides of backtracked RNA bind a conserved 'backtrack site' in the Pol II pore and funnel, trapping the active centre trigger loop and inhibiting mRNA elongation. In the reactivation intermediate, TFIIS locks the trigger loop away from backtracked RNA, displaces RNA from the backtrack site, and complements the polymerase active site with a basic and two acidic residues that may catalyse proton transfers during RNA cleavage. The active site is demarcated from the backtrack site by a 'gating tyrosine' residue that probably delimits backtracking. These results establish the structural basis of Pol II backtracking, arrest and reactivation, and provide a framework for analysing gene regulation during transcription elongation.


    Organizational Affiliation

    Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 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
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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
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
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G171Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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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
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor S-IIO [auth S]178Saccharomyces cerevisiaeMutation(s): 2 
Gene Names: DST1PPR2YGL043W
Find proteins for P07273 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
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  • Entity ID: 13
    MoleculeChainsLengthOrganismImage
    DNA non-template strandM [auth N]14N/A
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    • Entity ID: 14
      MoleculeChainsLengthOrganismImage
      RNA product strandN [auth P]5N/A
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      Entity ID: 16
      MoleculeChainsLengthOrganismImage
      DNA template strandP [auth T]27N/A
      Small Molecules
      Ligands 5 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      EPE
      Query on EPE

      Download Ideal Coordinates CCD File 
      U [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
      C8 H18 N2 O4 S
      JKMHFZQWWAIEOD-UHFFFAOYSA-N
       Ligand Interaction
      PGE
      Query on PGE

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      CA [auth L]TRIETHYLENE GLYCOL
      C6 H14 O4
      ZIBGPFATKBEMQZ-UHFFFAOYSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      AA [auth J] , BA [auth L] , DA [auth S] , Q [auth A] , R [auth A] , V [auth B] , X [auth C] , Y [auth I] , 
      AA [auth J],  BA [auth L],  DA [auth S],  Q [auth A],  R [auth A],  V [auth B],  X [auth C],  Y [auth I],  Z [auth I]
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      ACT
      Query on ACT

      Download Ideal Coordinates CCD File 
      T [auth A], W [auth B]ACETATE ION
      C2 H3 O2
      QTBSBXVTEAMEQO-UHFFFAOYSA-M
       Ligand Interaction
      MG
      Query on MG

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      S [auth A]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.30 Å
      • R-Value Free: 0.189 
      • R-Value Work: 0.161 
      • R-Value Observed: 0.162 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 220.019α = 90
      b = 395.067β = 90
      c = 280.429γ = 90
      Software Package:
      Software NamePurpose
      RemDAqdata collection
      PHASERphasing
      BUSTERrefinement
      MOSFLMdata reduction
      SCALAdata scaling

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2011-03-02
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2017-11-08
        Changes: Refinement description