1GCC

SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1GCC/pdb
• NAKB: 1GCC

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


• Deposited: 1998-03-13 Released: 1999-03-23 
• Deposition Author(s): Yamasaki, K., Allen, M.D., Ohme-Takagi, M., Tateno, M., Suzuki, M.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 1 
• Conformers Submitted: 1 

Literature

A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.

Allen, M.D., Yamasaki, K., Ohme-Takagi, M., Tateno, M., Suzuki, M.

(1998) EMBO J 17: 5484-5496

• PubMed: 9736626 
• DOI: https://doi.org/10.1093/emboj/17.18.5484
• Primary Citation of Related Structures:  
  1GCC, 2GCC, 3GCC


• PubMed Abstract: 
  

  The 3D solution structure of the GCC-box binding domain of a protein from Arabidopsis thaliana in complex with its target DNA fragment has been determined by heteronuclear multidimensional NMR in combination with simulated annealing and restrained molecular dynamic calculation. The domain consists of a three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet are identified to contact eight of the nine consecutive base pairs in the major groove, and at the same time bind to the sugar phosphate backbones. The target DNA bends slightly at the central CG step, thereby allowing the DNA to follow the curvature of the beta-sheet.

---

Organizational Affiliation: 

AIST-NIBHT Plant Molecular Biology Laboratory, Higashi 1-1, Tsukuba 305-0046, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.96 kDa 
• Atom Count: 958 
• Modelled Residue Count: 85 
• Deposited Residue Count: 85 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 1	C [auth A]	63	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ATERF1
UniProt
Find proteins for O80337 (Arabidopsis thaliana) Explore O80337  Go to UniProtKB:  O80337

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*CP*CP*GP*CP*CP*AP*GP*C)-3')	A [auth B]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*GP*CP*GP*GP*CP*TP*A)-3')	B [auth C]	11	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 1 
• Conformers Submitted: 1 

Structure Validation

Currently 1GCC does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 1999-03-23 
Deposition Author(s): Yamasaki, K., Allen, M.D., Ohme-Takagi, M., Tateno, M., Suzuki, M.

Revision History  

• Version 1.0: 1999-03-23
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Data collection, Structure summary