1I6H

RNA POLYMERASE II ELONGATION COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 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

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
A
1733Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO21 (RPB1, RPB220, SUA8)
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04050
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 140KD POLYPEPTIDE
B
1224Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB2 (RPB150, RPO22)
EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08518
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 45KD POLYPEPTIDE
C
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB3
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16370
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 27KD POLYPEPTIDE
E
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB5 (RPA7, RPC9)
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 23KD POLYPEPTIDE
F
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO26 (RPB6)
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 14.5KD POLYPEPTIDE
H
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB8
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20436
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 14.2KD POLYPEPTIDE
I
122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB9
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P27999
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 8.3KD POLYPEPTIDE
J
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB10
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 13.6KD POLYPEPTIDE
K
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB11
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38902
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II 7.7KD POLYPEPTIDE
L
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC10 (RPB12)
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(P*AP*AP*AP*TP*GP*CP*CP*TP*GP*GP*TP*CP*T)-3'D13Saccharomyces cerevisiae
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

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

Download SDF File 
Download CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.250 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 157.300α = 90.00
b = 220.700β = 97.50
c = 191.300γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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