3GTP

Backtracked RNA polymerase II complex with 24mer RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.

Wang, D.Bushnell, D.A.Huang, X.Westover, K.D.Levitt, M.Kornberg, R.D.

(2009) Science 324: 1203-1206

  • DOI: 10.1126/science.1168729
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Transcribing RNA polymerases oscillate between three stable states, two of which, pre- and posttranslocated, were previously subjected to x-ray crystal structure determination. We report here the crystal structure of RNA polymerase II in the third st ...

    Transcribing RNA polymerases oscillate between three stable states, two of which, pre- and posttranslocated, were previously subjected to x-ray crystal structure determination. We report here the crystal structure of RNA polymerase II in the third state, the reverse translocated, or "backtracked" state. The defining feature of the backtracked structure is a binding site for the first backtracked nucleotide. This binding site is occupied in case of nucleotide misincorporation in the RNA or damage to the DNA, and is termed the "P" site because it supports proofreading. The predominant mechanism of proofreading is the excision of a dinucleotide in the presence of the elongation factor SII (TFIIS). Structure determination of a cocrystal with TFIIS reveals a rearrangement whereby cleavage of the RNA may take place.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20436 
Go to UniProtKB:  P20436
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38902 
Go to UniProtKB:  P38902
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40422 
Go to UniProtKB:  P40422
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
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))
Explore P04050 
Go to UniProtKB:  P04050
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
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))
Explore P08518 
Go to UniProtKB:  P08518
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P16370 
Go to UniProtKB:  P16370
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20434 
Go to UniProtKB:  P20434
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20435 
Go to UniProtKB:  P20435
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P27999 
Go to UniProtKB:  P27999
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22139 
Go to UniProtKB:  P22139
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 11
MoleculeChainsLengthOrganism
RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*AP*UP*GP*CP*AP*GP*AP*CP*GP*UP*UP*UP*UP*UP*U)-3')R24N/A

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 12
MoleculeChainsLengthOrganism
DNA (28-MER)T28N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 13
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3')N14N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.268 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.778α = 90
b = 222.113β = 102.06
c = 194.854γ = 90
Software Package:
Software NamePurpose
MAR345data collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description