1I6H

RNA POLYMERASE II ELONGATION COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.

Gnatt, A.L.Cramer, P.Fu, J.Bushnell, D.A.Kornberg, R.D.

(2001) Science 292: 1876-1882

  • DOI: 10.1126/science.1059495
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from th ...

    The crystal structure of RNA polymerase II in the act of transcription was determined at 3.3 A resolution. Duplex DNA is seen entering the main cleft of the enzyme and unwinding before the active site. Nine base pairs of DNA-RNA hybrid extend from the active center at nearly right angles to the entering DNA, with the 3' end of the RNA in the nucleotide addition site. The 3' end is positioned above a pore, through which nucleotides may enter and through which RNA may be extruded during back-tracking. The 5'-most residue of the RNA is close to the point of entry to an exit groove. Changes in protein structure between the transcribing complex and free enzyme include closure of a clamp over the DNA and RNA and ordering of a series of "switches" at the base of the clamp to create a binding site complementary to the DNA-RNA hybrid. Protein-nucleic acid contacts help explain DNA and RNA strand separation, the specificity of RNA synthesis, "abortive cycling" during transcription initiation, and RNA and DNA translocation during transcription elongation.


    Related Citations: 
    • Structural Basis of Transcription: RNA Polymerase II at 2.8 A Resolution
      Cramer, P., Bushnell, D.A., Kornberg, R.D.
      (2001) Science 292: 1863
    • Architecture of RNA Polymerase II and Implications for the Transcription Mechanism
      Cramer, P., Bushnell, D.A., Fu, J., Gnatt, A.L., Maier-Davis, B., Thompson, N.E., Burgess, R.R., Edwards, A.M., David, P.R., Kornberg, R.D.
      (2000) Science 288: 640

    Organizational Affiliation

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



Macromolecules

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDEC318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 27KD POLYPEPTIDEE215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 23KD POLYPEPTIDEF155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 14.5KD POLYPEPTIDEH146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDEI122Saccharomyces 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 LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 8.3KD POLYPEPTIDEJ70Saccharomyces 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 LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDEK120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 7.7KD POLYPEPTIDEL70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNITA1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDEB1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(P*AP*AP*AP*TP*GP*CP*CP*TP*GP*GP*TP*CP*T)-3'D13Saccharomyces cerevisiae
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Entity ID: 2
MoleculeChainsLengthOrganism
5'-R(P*GP*AP*CP*CP*AP*GP*GP*CP*A)-3'R9N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.3α = 90
b = 220.7β = 97.5
c = 191.3γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-04-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation