1K6O

Crystal Structure of a Ternary SAP-1/SRF/c-fos SRE DNA Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.270 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a ternary SAP-1/SRF/c-fos SRE DNA complex.

Mo, Y.Ho, W.Johnston, K.Marmorstein, R.

(2001) J Mol Biol 314: 495-506

  • DOI: 10.1006/jmbi.2001.5138
  • Primary Citation of Related Structures:  
    1K6O

  • PubMed Abstract: 
  • Combinatorial DNA binding by proteins for promoter-specific gene activation is a common mode of DNA regulation in eukaryotic organisms, and occurs at the promoter of the c-fos proto-oncogene. The c-fos promoter contains a serum response element (SRE) ...

    Combinatorial DNA binding by proteins for promoter-specific gene activation is a common mode of DNA regulation in eukaryotic organisms, and occurs at the promoter of the c-fos proto-oncogene. The c-fos promoter contains a serum response element (SRE) that mediates ternary complex formation with the Ets proteins SAP-1 or Elk-1 and the MADS-box protein, serum response factor (SRF). Here, we report the crystal structure of a ternary SAP-1/SRF/c-fos SRE DNA complex containing the minimal DNA-binding domains of each protein. The structure of the complex reveals that the SAP-1 monomer and SRF dimer are bound on opposite faces of the DNA, and that the DNA recognition helix of SAP-1 makes direct contact with the DNA recognition helix of one of the two SRF subunits. These interactions facilitate an 82 degrees DNA bend around SRF and a modulation of protein-DNA contacts by each protein when compared to each of the binary DNA complexes. A comparison with a recently determined complex containing SRF, an idealized DNA site, and a SAP-1 fragment containing a SRF-interacting B-box region, shows a similar overall architecture but also shows important differences. Specifically, the comparison suggests that the B-box region of the Ets protein does not significantly influence DNA recognition by either of the proteins, and that the sequence of the DNA target effects the way in which the two proteins cooperate for DNA recognition. These studies have implications for how DNA-bound SRF may modulate the DNA-binding properties of other Ets proteins such as Elk-1, and for how other Ets proteins may modulate the DNA-binding properties of other DNA-bound accessory factors to facilitate promoter-specific transcriptional responses.


    Organizational Affiliation

    The Wistar Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ETS-domain protein ELK-4A93Homo sapiensMutation(s): 0 
Gene Names: SapELK4SAP1
Find proteins for P28324 (Homo sapiens)
Explore P28324 
Go to UniProtKB:  P28324
NIH Common Fund Data Resources
PHAROS  P28324
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Serum response factorBC103Homo sapiensMutation(s): 0 
Gene Names: SRF
Find proteins for P11831 (Homo sapiens)
Explore P11831 
Go to UniProtKB:  P11831
NIH Common Fund Data Resources
PHAROS  P11831
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*AP*CP*AP*GP*GP*AP*TP*GP*TP*CP*CP*AP*TP*AP*TP*TP*AP*GP*GP*AP*CP*A)-3'D23N/A
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*TP*GP*TP*CP*CP*TP*AP*AP*TP*AP*TP*GP*GP*AP*CP*AP*TP*CP*CP*TP*GP*TP*G)-3'E23N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.270 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.784α = 90
b = 161.784β = 90
c = 41.224γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation