X-ray crystal structure of the N4 mini-vRNAP P2_7a promoter complex soaked with MgCl2

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 

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Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.

Gleghorn, M.L.Davydova, E.K.Rothman-Denes, L.B.Murakami, K.S.

(2008) Mol Cell 32: 707-717

  • DOI: https://doi.org/10.1016/j.molcel.2008.11.010
  • Primary Citation of Related Structures:  
    3C2P, 3C3L, 3C46

  • PubMed Abstract: 

    Coliphage N4 virion-encapsidated RNA polymerase (vRNAP) is a member of the phage T7-like single-subunit RNA polymerase (RNAP) family. Its central domain (mini-vRNAP) contains all RNAP functions of the full-length vRNAP, which recognizes a 5 to 7 base pair stem and 3 nucleotide loop hairpin DNA promoter. Here, we report the X-ray crystal structures of mini-vRNAP bound to promoters. Mini-vRNAP uses four structural motifs to recognize DNA sequences at the hairpin loop and stem and to unwind DNA. Despite their low sequence similarity, three out of four motifs are shared with T7 RNAP that recognizes a double-stranded DNA promoter. The binary complex structure and results of engineered disulfide linkage experiments reveal that the plug and motif B loop, which block the access of template DNA to the active site in the apo-form mini-vRNAP, undergo a large-scale conformational change upon promoter binding, explaining the restricted promoter specificity that is critical for N4 phage early transcription.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Virion RNA polymeraseA,
C [auth B]
1,117N/AMutation(s): 0 
Gene Names: vRNAP
Find proteins for Q859P9 (Enterobacteria phage N4)
Explore Q859P9 
Go to UniProtKB:  Q859P9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ859P9
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
P2_7a Promoter DNAB [auth C],
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.622α = 90
b = 111.424β = 90
c = 276.763γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description