3E2E

Crystal Structure of an Intermediate Complex of T7 RNAP and 7nt of RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of a transcribing t7 RNA polymerase in transition from initiation to elongation

Durniak, K.J.Bailey, S.Steitz, T.A.

(2008) Science 322: 553-557

  • DOI: 10.1126/science.1163433
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Structural studies of the T7 bacteriophage DNA-dependent RNA polymerase (T7 RNAP) have shown that the conformation of the amino-terminal domain changes substantially between the initiation and elongation phases of transcription, but how this transiti ...

    Structural studies of the T7 bacteriophage DNA-dependent RNA polymerase (T7 RNAP) have shown that the conformation of the amino-terminal domain changes substantially between the initiation and elongation phases of transcription, but how this transition is achieved remains unclear. We report crystal structures of T7 RNAP bound to promoter DNA containing either a 7- or an 8-nucleotide (nt) RNA transcript that illuminate intermediate states along the transition pathway. The amino-terminal domain comprises the C-helix subdomain and the promoter binding domain (PBD), which consists of two segments separated by subdomain H. The structures of the intermediate complex reveal that the PBD and the bound promoter rotate by approximately 45 degrees upon synthesis of an 8-nt RNA transcript. This allows the promoter contacts to be maintained while the active site is expanded to accommodate a growing heteroduplex. The C-helix subdomain moves modestly toward its elongation conformation, whereas subdomain H remains in its initiation- rather than its elongation-phase location, more than 70 angstroms away.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06520-8114, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase
A
889Enterobacteria phage T7Mutation(s): 1 
Find proteins for P00573 (Enterobacteria phage T7)
Go to UniProtKB:  P00573
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*GP*AP*GP*UP*G)-3')R7synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (31-MER)T33synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (28-MER)N33synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 81.008α = 90.00
b = 81.008β = 90.00
c = 358.791γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Data collection, Refinement description, Source and taxonomy