1Y1Y

RNA Polymerase II-TFIIS-DNA/RNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Work: 0.281 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.

Kettenberger, H.Armache, K.J.Cramer, P.

(2004) Mol Cell 16: 955-965

  • DOI: https://doi.org/10.1016/j.molcel.2004.11.040
  • Primary Citation of Related Structures:  
    1Y1V, 1Y1W, 1Y1Y, 1Y77

  • PubMed Abstract: 

    The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.


  • Organizational Affiliation

    Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II largest subunitC [auth A]1,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 140 kDa polypeptideD [auth B]1,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 45 kDa polypeptideE [auth C]318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 32 kDa polypeptideF [auth D]221Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptideG [auth E]215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 8
MoleculeChains Sequence 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
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 19 kDa polypeptideI [auth G]171Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptideJ [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit 9K [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I/II/III subunit 10L [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 13.6 kDa polypeptideM [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptideN [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor S-IIO [auth S]179Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: DST1
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(P*TP*AP*CP*GP*CP*CP*T)-3'A [auth T]7N/A
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-R(P*AP*GP*GP*C)-3'B [auth P]4N/A
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Work: 0.281 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.2α = 90
b = 395.7β = 90
c = 282.1γ = 90

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references