2NVZ

RNA Polymerase II elongation complex with UTP, updated 11/2006


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.332 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.276 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis

Wang, D.Bushnell, D.A.Westover, K.D.Kaplan, C.D.Kornberg, R.D.

(2006) Cell 127: 941-954

  • DOI: 10.1016/j.cell.2006.11.023
  • Primary Citation of Related Structures:  
    2E2J, 2E2I, 2E2H, 2YU9, 2NVQ, 2NVY, 2NVX, 2NVT, 2NVZ

  • PubMed Abstract: 
  • New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues ...

    New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II largest subunitD [auth A]1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04050 
Go to UniProtKB:  P04050
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 140 kDa polypeptideE [auth B]1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P08518 
Go to UniProtKB:  P08518
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P16370 
Go to UniProtKB:  P16370
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20434 
Go to UniProtKB:  P20434
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20435 
Go to UniProtKB:  P20435
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20436 
Go to UniProtKB:  P20436
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit 9J [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P27999 
Go to UniProtKB:  P27999
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I/II/III subunit 10K [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22139 
Go to UniProtKB:  P22139
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38902 
Go to UniProtKB:  P38902
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
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
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40422 
Go to UniProtKB:  P40422
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'A [auth R]10synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Find similar nucleic acids by:  (by identity cutoff)  |  Structure
    Entity ID: 2
    MoleculeChainsLengthOrganismImage
    28-MER DNA template strandB [auth T]28synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3'C [auth N]14synthetic construct
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 4.30 Å
      • R-Value Free: 0.332 
      • R-Value Work: 0.270 
      • R-Value Observed: 0.276 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 169.647α = 90
      b = 222.338β = 101.67
      c = 194.316γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      PDB_EXTRACTdata extraction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2006-12-19
        Type: Initial release
      • Version 1.1: 2007-10-16
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2019-12-11
        Changes: Advisory, Derived calculations, Source and taxonomy