7JSL

Crystal structure of the DNA binding domain of human transcription factor ERF in the oxidized form, in complex with double-stranded DNA ACCGGAAGTG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.51 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Literature

Structural Insight into the DNA Binding Function of Transcription Factor ERF.

Hou, C.McCown, C.Ivanov, D.N.Tsodikov, O.V.

(2020) Biochemistry 

  • DOI: 10.1021/acs.biochem.0c00774
  • Primary Citation of Related Structures:  
    7JSA, 7JSL

  • PubMed Abstract: 
  • ETS family transcription factors control development of different cell types in humans, whereas deregulation of these proteins leads to severe developmental syndromes and cancers. One of a few members of the ETS family that are known to act solely as repressors, ERF, is required for normal osteogenesis and hematopoiesis ...

    ETS family transcription factors control development of different cell types in humans, whereas deregulation of these proteins leads to severe developmental syndromes and cancers. One of a few members of the ETS family that are known to act solely as repressors, ERF, is required for normal osteogenesis and hematopoiesis. Another important function of ERF is acting as a tumor suppressor by antagonizing oncogenic fusions involving other ETS family factors. The structure of ERF and the DNA binding properties specific to this protein have not been elucidated. In this study, we determined two crystal structures of the complexes of the DNA binding domain of ERF with DNA. In one, ERF is in a distinct dimeric form, with Cys72 in a reduced state. In the other, two dimers of ERF are assembled into a tetramer that is additionally locked by two Cys72-Cys72 disulfide bonds across the dimers. In the tetramer, the ERF molecules are bound to a pseudocontinuous DNA on the same DNA face at two GGAA binding sites on opposite strands. Sedimentation velocity analysis showed that this tetrameric assembly forms on continuous DNA containing such tandem sites spaced by 7 bp. Our bioinformatic analysis of three previously reported sets of ERF binding loci across entire genomes showed that these loci were enriched in such 7 bp spaced tandem sites. Taken together, these results strongly suggest that the observed tetrameric assembly is a functional state of ERF in the human cell.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ETS domain-containing transcription factor ERFF [auth E], I [auth H], C [auth J], L123Homo sapiensMutation(s): 0 
Gene Names: ERF
UniProt & NIH Common Fund Data Resources
Find proteins for P50548 (Homo sapiens)
Explore P50548 
Go to UniProtKB:  P50548
PHAROS:  P50548
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*CP*GP*GP*AP*AP*GP*TP*G)-3')D [auth A], A [auth B], G [auth F], J [auth I]10synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*CP*AP*CP*TP*TP*CP*CP*GP*GP*T)-3')B [auth C], E [auth D], H [auth G], K10synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.51 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.537α = 90
b = 128.464β = 90
c = 174.914γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Defense (DOD, United States)United StatesPC150300
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA243529

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release