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 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1016/s0092-8674(03)00887-0
  • Primary Citation of Related Structures:  
    1PP7, 1PP8, 1Q87, 1Q88, 1Q89

  • 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). 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

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
39 kDa initiator binding proteinC [auth U]131Trichomonas vaginalisMutation(s): 0 
Gene Names: Trichomonas vaginalis:IBP39
UniProt
Find proteins for Q95VR4 (Trichomonas vaginalis)
Explore Q95VR4 
Go to UniProtKB:  Q95VR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ95VR4
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
FERREDOXIN INRA [auth E]13N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
FERREDOXIN INRB [auth F]13N/A
Sequence Annotations
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  • 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

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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
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description