1PUE

PU.1 ETS DOMAIN-DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex.

Kodandapani, R.Pio, F.Ni, C.Z.Piccialli, G.Klemsz, M.McKercher, S.Maki, R.A.Ely, K.R.

(1996) Nature 380: 456-460

  • DOI: 10.1038/380456a0
  • Primary Citation of Related Structures:  
    1PUE

  • PubMed Abstract: 
  • The Ets family of transcription factors, of which there are now about 35 members regulate gene expression during growth and development. They share a conserved domain of around 85 amino acids which binds as a monomer to the DNA sequence 5'-C/AGGAA/T- ...

    The Ets family of transcription factors, of which there are now about 35 members regulate gene expression during growth and development. They share a conserved domain of around 85 amino acids which binds as a monomer to the DNA sequence 5'-C/AGGAA/T-3'. We have determined the crystal structure of an ETS domain complexed with DNA, at 2.3-A resolution. The domain is similar to alpha + beta (winged) 'helix-turn-helix' proteins and interacts with a ten-base-pair region of duplex DNA which takes up a uniform curve of 8 degrees. The domain contacts the DNA by a novel loop-helix-loop architecture. Four of amino acids that directly interact with the DNA are highly conserved: two arginines from the recognition helix lying in the major groove, one lysine from the 'wing' that binds upstream of the core GGAA sequence, and another lysine, from the 'turn' of the 'helix-turn-helix' motif, which binds downstream and on the opposite strand.


    Related Citations: 
    • New Insights on DNA Recognition by ETS Proteins from the Crystal Structure of the PU.1 ETS Domain-DNA Complex
      Pio, F., Kodandapani, R., Ni, C.Z., Shepard, W., Klemsz, M., McKercher, S.R., Maki, R.A., Ely, K.R.
      (1996) J Biol Chem 271: 23329

    Organizational Affiliation

    La Jolla Cancer Research Center at the Burnham Institute, California 92037, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))EF89Mus musculusMutation(s): 0 
Gene Names: Spi1Sfpi-1Sfpi1
Find proteins for P17433 (Mus musculus)
Explore P17433 
Go to UniProtKB:  P17433
NIH Common Fund Data Resources
IMPC  MGI:98282
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*AP*AP*AP*AP*GP*GP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')A, C16synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*CP*CP*TP*TP*TP*T)-3')B, D16synthetic construct
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.10 Å
      • R-Value Free: 0.287 
      • R-Value Work: 0.225 
      • R-Value Observed: 0.225 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 89.1α = 90
      b = 101.9β = 111.2
      c = 55.6γ = 90
      Software Package:
      Software NamePurpose
      X-PLORrefinement
      MOSFLMdata reduction

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 1997-02-12
        Type: Initial release
      • Version 1.1: 2008-05-22
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2017-02-15
        Changes: Source and taxonomy, Structure summary