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 

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

  • Primary Citation of Related Structures:  1PP7, 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 line ...

    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
39 kDa initiator binding protein
U, P, F, V, M, O
132Trichomonas vaginalisGene Names: IBP39
Find proteins for Q95VR4 (Trichomonas vaginalis)
Go to UniProtKB:  Q95VR4
Entity ID: 1
MoleculeChainsLengthOrganism
ALPHA-SCS INRE,I,Y,K12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
ALPHA-SCS INRT,R,J,G12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
O, V
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 
  • Space Group: F 2 3
Unit Cell:
Length (Å)Angle (°)
a = 292.000α = 90.00
b = 292.000β = 90.00
c = 292.000γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SOLVEphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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