4IRI | pdb_00004iri

Auto-inhibited ERG Ets Domain-DNA Complex

• PDB DOI: https://doi.org/10.2210/pdb4IRI/pdb
• NAKB: 4IRI

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-01-14 Released: 2013-07-31 
• Deposition Author(s): Regan, M.C., Horanyi, P.S., Pryor, E.E., Sarver, J.L., Cafiso, D.S., Bushweller, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free: 
  0.210 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

Structural and dynamic studies of the transcription factor ERG reveal DNA binding is allosterically autoinhibited.

Regan, M.C., Horanyi, P.S., Pryor, E.E., Sarver, J.L., Cafiso, D.S., Bushweller, J.H.

(2013) Proc Natl Acad Sci U S A 110: 13374-13379

• PubMed: 23898196 
• DOI: https://doi.org/10.1073/pnas.1301726110
• Primary Citation Related Structures: 
  4IRG, 4IRH, 4IRI


• PubMed Abstract: 
  

  The Ets-Related Gene (ERG) belongs to the Ets family of transcription factors and is critically important for maintenance of the hematopoietic stem cell population. A chromosomal translocation observed in the majority of human prostate cancers leads to the aberrant overexpression of ERG. We have identified regions flanking the ERG Ets domain responsible for autoinhibition of DNA binding and solved crystal structures of uninhibited, autoinhibited, and DNA-bound ERG. NMR-based measurements of backbone dynamics show that uninhibited ERG undergoes substantial dynamics on the millisecond-to-microsecond timescale but autoinhibited and DNA-bound ERG do not. We propose a mechanism whereby the allosteric basis of ERG autoinhibition is mediated predominantly by the regulation of Ets-domain dynamics with only modest structural changes.

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Organizational Affiliation: 
• Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.2 kDa 
• Atom Count: 1,272 
• Modeled Residue Count: 118 
• Deposited Residue Count: 153 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator ERG	A	129	Homo sapiens	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*G)-3')	B	12	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*C)-3')	C	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.77 Å
• R-Value Free:  0.210 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.486	α = 90
b = 51.486	β = 90
c = 141.313	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Regan, M.C., Horanyi, P.S., Pryor, E.E., Sarver, J.L., Cafiso, D.S., Bushweller, J.H.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Database references
• Version 1.2: 2013-08-28
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references