1IMH | pdb_00001imh

TonEBP/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1IMH/pdb
• NAKB: 1IMH

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


• Deposited: 2001-05-10 Released: 2002-02-01 
• Deposition Author(s): Stroud, J.C., Lopez-Rodriguez, C., Rao, A., Chen, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.290 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

Literature

Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor.

Stroud, J.C., Lopez-Rodriguez, C., Rao, A., Chen, L.

(2002) Nat Struct Biol 9: 90-94

• PubMed: 11780147 
• DOI: https://doi.org/10.1038/nsb749
• Primary Citation Related Structures: 
  1IMH


• PubMed Abstract: 
  

  Tonicity-responsive enhancer binding protein (TonEBP), also known as NFAT5, is a unique member of the NFAT family of transcription factors that regulates gene expression induced by osmotic stress in mammalian cells. Unlike monomeric members of the NFAT family, TonEBP exists as a homodimer and binds asymmetric TonE DNA sites; furthermore, the affinity of TonEBP for DNA is much lower than that of other NFAT proteins. How TonEBP recognizes the TonE site and regulates the activation of hypertonicity response genes has not been clear. Here we show that TonEBP adopts a NF-kappaB-like structure upon binding to DNA, providing a direct structural link between the NFAT and NF-kappaB family of transcription factors. We also show that TonEBP completely encircles its DNA target and present biochemical evidence that the DNA encirclement may lead to increased kinetic stability of the TonEBP-DNA complex. Thus, the list of proteins that bind DNA by encirclement is now expanded to include sequence-specific transcription factors.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.44 kDa 
• Atom Count: 4,977 
• Modeled Residue Count: 592 
• Deposited Residue Count: 592 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR FACTOR OF ACTIVATED T CELLS 5	C, D	281	Homo sapiens	Mutation(s): 0  Gene Names: NFAT5
UniProt & NIH Common Fund Data Resources
Find proteins for O94916 (Homo sapiens) Explore O94916  Go to UniProtKB:  O94916
PHAROS:  O94916 GTEx:  ENSG00000102908

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3'	A	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3'	B	15	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.290 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.568	α = 90
b = 95.368	β = 90
c = 158.431	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-01 
Deposition Author(s): Stroud, J.C., Lopez-Rodriguez, C., Rao, A., Chen, L.

Revision History  

• Version 1.0: 2002-02-01
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references, Refinement description