5YBC

X-ray structure of native ETS-domain domain of Ergp55


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Comparative structure analysis of the ETSi domain of ERG3 and its complex with the E74 promoter DNA sequence

Sharma, R.Gangwar, S.P.Saxena, A.K.

(2018) Acta Crystallogr F Struct Biol Commun 74: 656-663

  • DOI: 10.1107/S2053230X1801110X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • ERG3 (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors, which contain a highly conserved DNA-binding domain. The ETS family of transcription factors differ in their binding to promoter DN ...

    ERG3 (ETS-related gene) is a member of the ETS (erythroblast transformation-specific) family of transcription factors, which contain a highly conserved DNA-binding domain. The ETS family of transcription factors differ in their binding to promoter DNA sequences, and the mechanism of their DNA-sequence discrimination is little known. In the current study, crystals of the ETSi domain (the ETS domain of ERG3 containing a CID motif) in space group P4 1 2 1 2 and of its complex with the E74 DNA sequence (DNA 9 ) in space group C222 1 were obtained and their structures were determined. Comparative structure analysis of the ETSi domain and its complex with DNA 9 with previously determined structures of the ERGi domain (the ETS domain of ERG containing inhibitory motifs) in space group P6 5 2 1 2 and of the ERGi-DNA 12 complex in space group P4 1 2 1 2 were performed. The ETSi domain is observed as a homodimer in solution as well as in the crystallographic asymmetric unit. Superposition of the structure of the ETSi domain on that of the ERGi domain showed a major conformational change at the C-terminal DNA-binding autoinhibitory (CID) motif, while minor changes are observed in the loop regions of the ETSi-domain structure. The ETSi-DNA 9 complex in space group C222 1 forms a structure that is quite similar to that of the ERG-DNA 12 complex in space group P4 1 2 1 2. Upon superposition of the complexes, major conformational changes are observed at the 5' and 3' ends of DNA 9 , while the conformation of the core GGA nucleotides was quite conserved. Comparison of the ETSi-DNA 9 structure with known structures of ETS class 1 protein-DNA complexes shows the similarities and differences in the promoter DNA binding and specificity of the class 1 ETS proteins.


    Organizational Affiliation

    Structural Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110 067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator ERG
C, A
92Homo sapiensMutation(s): 0 
Gene Names: ERG
Find proteins for P11308 (Homo sapiens)
Go to Gene View: ERG
Go to UniProtKB:  P11308
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.565α = 90.00
b = 64.565β = 90.00
c = 128.305γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata collection
PHENIXrefinement
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Science & TechnologyIndiaSR/SO/HS-05/2009

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-10-17
    Type: Data collection, Database references