1PP7

Crystal structure of the T. vaginalis Initiator binding protein bound to the ferredoxin Inr


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Core Promoter Recognition in a Primitive Eukaryote

Schumacher, M.A.Lau, A.O.T.Johnson, P.J.

(2003) Cell 115: 413-424

  • DOI: 10.1016/s0092-8674(03)00887-0
  • Primary Citation of Related Structures:  
    1Q87, 1Q89, 1Q88, 1PP8, 1PP7

  • PubMed Abstract: 
  • Transcription start site selection in eukaryotes is mediated through combinations of the TATA, initiator (Inr), and downstream promoter elements (DPE). In Trichomonas vaginalis, a parabasalian flagellate thought to represent an ancient eukaryote lineage, the Inr appears to be solely responsible for start site selection and is recognized by the initiator binding protein 39 kDa (IBP39) ...

    Transcription start site selection in eukaryotes is mediated through combinations of the TATA, initiator (Inr), and downstream promoter elements (DPE). In Trichomonas vaginalis, a parabasalian flagellate thought to represent an ancient eukaryote lineage, the Inr appears to be solely responsible for start site selection and is recognized by the initiator binding protein 39 kDa (IBP39). IBP39 contains an N-terminal Inr binding domain (IBD) connected via a flexible linker to a C-terminal domain (C domain). Here we present crystal structures of the apoIBD and IBD-Inr complexes and the C domain. The IBD structures reveal a winged-helix motif with prokaryotic and eukaryotic features and a scaffold similar to that of ETS-family proteins. The C domain structure and biochemical studies indicate that it interacts with the T. vaginalis RNAP II large subunit C-terminal domain. These data suggest that binding of IBP39 to the Inr directly recruits RNAP II and in this way initiates transcription.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA. schumacm@ohsu.edu



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
39 kDa initiator binding proteinC [auth U]131Trichomonas vaginalisMutation(s): 0 
Gene Names: Trichomonas vaginalis:IBP39IBP39TVAG_455080
UniProt
Find proteins for Q95VR4 (Trichomonas vaginalis)
Explore Q95VR4 
Go to UniProtKB:  Q95VR4
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    FERREDOXIN INRA [auth E]13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      FERREDOXIN INRB [auth F]13N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.45 Å
      • R-Value Free: 0.246 
      • R-Value Work: 0.197 
      • R-Value Observed: 0.197 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 81.34α = 90
      b = 41.43β = 90
      c = 58.39γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      MOSFLMdata reduction
      CCP4data scaling
      MOLREPphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2003-11-18
        Type: Initial release
      • Version 1.1: 2008-04-29
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance