3E2E

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

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
  • Structures With Same Primary Citation

  • 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 transition is achieved remains unclear ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymeraseA889Escherichia phage T7Mutation(s): 1 
Gene Names: 1
EC: 2.7.7.6
Find proteins for P00573 (Escherichia phage T7)
Explore P00573 
Go to UniProtKB:  P00573
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*GP*AP*GP*UP*G)-3')R7synthetic construct

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Entity ID: 3
MoleculeChainsLengthOrganism
DNA (31-MER)T33synthetic construct

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Entity ID: 4
MoleculeChainsLengthOrganism
DNA (28-MER)N33synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.008α = 90
b = 81.008β = 90
c = 358.791γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History 

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