5YBD

X-ray structure of ETS domain of Ergp55 in complex with E74DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


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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: https://doi.org/10.1107/S2053230X1801110X
  • Primary Citation of Related Structures:  
    5YBC, 5YBD

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator ERGA,
D [auth X]
97Homo sapiensMutation(s): 0 
Gene Names: ERG
UniProt & NIH Common Fund Data Resources
Find proteins for P11308 (Homo sapiens)
Explore P11308 
Go to UniProtKB:  P11308
PHAROS:  P11308
GTEx:  ENSG00000157554 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11308
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*AP*CP*CP*GP*GP*AP*AP*GP*T)-3')B,
E [auth Y]
9Drosophila saltans
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')C,
F [auth Z]
10Drosophila adunca
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.279α = 90
b = 233.871β = 90
c = 80.524γ = 90
Software Package:
Software NamePurpose
DENZOdata collection
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Advisory, Data collection, Database references