1DUX

ELK-1/DNA STRUCTURE REVEALS HOW RESIDUES DISTAL FROM DNA-BINDING SURFACE AFFECT DNA-RECOGNITION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA.

Mo, Y.Vaessen, B.Johnston, K.Marmorstein, R.

(2000) Nat.Struct.Mol.Biol. 7: 292-297

  • DOI: 10.1038/74055

  • PubMed Abstract: 
  • SAP-1 and Elk-1 are members of a large group of eukaryotic transcription factors that contain a conserved ETS DNA binding domain and that cooperate with the serum response factor (SRF) to activate transcription of the c-fos protooncogene. Despite the ...

    SAP-1 and Elk-1 are members of a large group of eukaryotic transcription factors that contain a conserved ETS DNA binding domain and that cooperate with the serum response factor (SRF) to activate transcription of the c-fos protooncogene. Despite the high degree of sequence similarity, which includes an identical amino acid sequence for the DNA recognition helix within the ETS domain of these proteins, they exhibit different DNA binding properties. Here we report the 2.1 ¿ crystal structure of the ETS domain of Elk-1 bound to a high affinity E74 DNA (E74DNA) site and compare it to a SAP-1-E74DNA complex. This comparison reveals that the differential DNA binding properties of these proteins are mediated by non-conserved residues distal to the DNA binding surface that function to orient conserved residues in the DNA recognition helix for protein-specific DNA contacts. As a result, nearly one-third of the interactions between the protein recognition helix and the DNA are different between the SAP-1 and Elk-1 DNA complexes. Taken together, these studies reveal a novel mechanism for the modulation of DNA binding specificity within a conserved DNA binding domain, and have implications for how highly homologous ETS proteins exhibit differential DNA-binding properties.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ETS-DOMAIN PROTEIN ELK-1
C, F
94Homo sapiensMutation(s): 0 
Gene Names: ELK1
Find proteins for P19419 (Homo sapiens)
Go to Gene View: ELK1
Go to UniProtKB:  P19419
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3')A,D13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3')B,E13N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 33.245α = 90.00
b = 140.523β = 115.52
c = 38.620γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance