1PP8

crystal structure of the T. vaginalis IBP39 Initiator binding domain (IBD) bound to the alpha-SCS Inr element

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 

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:  
    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) ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
39 kDa initiator binding protein132Trichomonas vaginalisMutation(s): 0 
Gene Names: Trichomonas vaginalis:IBP39, IBP39, TVAG_455080
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
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
ALPHA-SCS INRA [auth E],
B [auth I],
D [auth K],
C [auth Y]		12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
ALPHA-SCS INRH [auth G],
G [auth J],
F [auth R],
E [auth T]		12N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
O [auth V],
P [auth O]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.269 
  • Space Group: F 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 292α = 90
b = 292β = 90
c = 292γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing

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