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-3'. We have determined the crystal structure of an ETS domain complexed with DNA, at 2 ...

    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

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (TRANSCRIPTION FACTOR PU.1 (TF PU.1))E, F89Mus musculusMutation(s): 0 
Gene Names: Spi1, Sfpi-1, Sfpi1
UniProt & NIH Common Fund Data Resources
Find proteins for P17433 (Mus musculus)
Explore P17433 
Go to UniProtKB:  P17433
IMPC:  MGI:98282
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17433
Protein Feature View
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  • Reference Sequence

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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
Protein Feature View
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  • Reference Sequence

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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
Protein Feature View
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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