1A02 | pdb_00001a02

STRUCTURE OF THE DNA BINDING DOMAINS OF NFAT, FOS AND JUN BOUND TO DNA

• PDB DOI: https://doi.org/10.2210/pdb1A02/pdb
• NAKB: 1A02

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 1997-12-08 Released: 1998-05-27 
• Deposition Author(s): Chen, L., Glover, J.N.M., Hogan, P.G., Rao, A., Harrison, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.303 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Literature

Structure of the DNA-binding domains from NFAT, Fos and Jun bound specifically to DNA.

Chen, L., Glover, J.N., Hogan, P.G., Rao, A., Harrison, S.C.

(1998) Nature 392: 42-48

• PubMed: 9510247 
• DOI: https://doi.org/10.1038/32100
• Primary Citation Related Structures: 
  1A02


• PubMed Abstract: 
  

  The nuclear factor of activated T cells (NFAT) and the AP-1 heterodimer, Fos-Jun, cooperatively bind a composite DNA site and synergistically activate the expression of many immune-response genes. A 2.7-A-resolution crystal structure of the DNA-binding domains of NFAT, Fos and Jun, in a quaternary complex with a DNA fragment containing the distal antigen-receptor response element from the interleukin-2 gene promoter, shows an extended interface between NFAT and AP-1, facilitated by the bending of Fos and DNA. The tight association of the three proteins on DNA creates a continuous groove for the recognition of 15 base pairs.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content 

• Total Structure Weight: 59.85 kDa 
• Atom Count: 3,974 
• Modeled Residue Count: 425 
• Deposited Residue Count: 453 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEAR FACTOR OF ACTIVATED T CELLS	C [auth N]	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 FRAGMENT FOS	D [auth F]	56	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P01100 (Homo sapiens) Explore P01100  Go to UniProtKB:  P01100
PHAROS:  P01100 GTEx:  ENSG00000170345

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 FRAGMENT JUN	E [auth J]	56	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P05412 (Homo sapiens) Explore P05412  Go to UniProtKB:  P05412
PHAROS:  P05412 GTEx:  ENSG00000177606

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DTP*DTP*DGP*DGP*DAP*DAP*DAP*DAP*DTP*DTP*DTP*DGP*DTP*DTP*DTP*DCP*DAP*DTP*DAP*DG)-3')	A	20	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DAP*DAP*DCP*DTP*DAP*DTP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DTP*DTP*DTP*DTP*DCP*DC)-3')	B	20	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.303 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.66	α = 90
b = 85.46	β = 112.03
c = 83.37	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
CCP4	phasing
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-05-27 
Deposition Author(s): Chen, L., Glover, J.N.M., Hogan, P.G., Rao, A., Harrison, S.C.

Revision History  

• Version 1.0: 1998-05-27
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references
• Version 1.4: 2024-02-07
  Changes: Data collection