1PZU

An asymmetric NFAT1-RHR homodimer on a pseudo-palindromic, Kappa-B site

• PDB DOI: https://doi.org/10.2210/pdb1PZU/pdb
• NAKB: 1PZU

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-07-14 Released: 2003-09-09 
• Deposition Author(s): Jin, L., Sliz, P., Chen, L., Macian, F., Rao, A., Hogan, P.G., Harrison, S.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.319 
• R-Value Work: 0.296 
• R-Value Observed: 0.303 

Literature

An asymmetric NFAT1 dimer on a pseudo-palindromic KB-like DNA site

Jin, L., Sliz, P., Chen, L., Macian, F., Rao, A., Hogan, P.G., Harrison, S.C.

(2003) Nat Struct Biol 10: 807-811

• PubMed: 12949491 
• DOI: https://doi.org/10.1038/nsb975
• Primary Citation of Related Structures:  
  1PZU


• PubMed Abstract: 
  

  The crystal structure of the NFAT1 Rel homology region (RHR) bound to a pseudo-palindromic DNA site reveals an asymmetric dimer interaction between the RHR-C domains, unrelated to the contact seen in Rel dimers such as NF kappa B. Binding studies with a form of the NFAT1 RHR defective in the dimer contact show loss of cooperativity and demonstrate that the same interaction is present in solution. The structure we have determined may correspond to a functional NFAT binding mode at palindromic sites of genes induced during the anergic response to weak TCR signaling.

---

Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology and Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 231.3 kDa 
• Atom Count: 14,952 
• Modelled Residue Count: 1,740 
• Deposited Residue Count: 1,890 
• 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, cytoplasmic 2	G [auth B], H [auth D], I [auth H], J [auth I], K [auth L], L [auth M]	301	Homo sapiens	Mutation(s): 0  Gene Names: NFAT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13469 (Homo sapiens) Explore Q13469  Go to UniProtKB:  Q13469
PHAROS:  Q13469 GTEx:  ENSG00000101096

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*TP*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*A)-3'	A [auth X], C [auth V], E [auth T]	14	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*AP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3'	B [auth Y], D [auth Z], F [auth W]	14	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.319 
• R-Value Work: 0.296 
• R-Value Observed: 0.303 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.7	α = 90
b = 122.9	β = 90
c = 241.6	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-09-09 
Deposition Author(s): Jin, L., Sliz, P., Chen, L., Macian, F., Rao, A., Hogan, P.G., Harrison, S.C.

Revision History  

• Version 1.0: 2003-09-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references