1UL5

Solution structure of the DNA-binding domain of squamosa promoter binding protein-like 7


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations, structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors.

Yamasaki, K.Kigawa, T.Inoue, M.Tateno, M.Yamasaki, T.Yabuki, T.Aoki, M.Seki, E.Matsuda, T.Nunokawa, E.Ishizuka, Y.Terada, T.Shirouzu, M.Osanai, T.Tanaka, A.Seki, M.Shinozaki, K.Yokoyama, S.

(2004) J.Mol.Biol. 337: 49-63

  • DOI: 10.1016/j.jmb.2004.01.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SQUAMOSA promoter binding proteins (SBPs) form a major family of plant-specific transcription factors related to flower development. Although SBPs are heterogeneous in primary structure, they share a highly conserved DNA-binding domain (DBD) that has ...

    SQUAMOSA promoter binding proteins (SBPs) form a major family of plant-specific transcription factors related to flower development. Although SBPs are heterogeneous in primary structure, they share a highly conserved DNA-binding domain (DBD) that has been suggested to be zinc binding. Here we report the NMR solution structures of DBDs of two SBPs of Arabidopsis thaliana, SPL4 and SPL7. The two share essentially the same structural features. Each structure contains two zinc-binding sites consisting of eight Cys or His residues in a Cys3HisCys2HisCys or Cys6HisCys sequence motif in which the first four residues coordinate to one zinc and the last four coordinate to the other. These structures are dissimilar to other known zinc-binding structures, and thus represent a novel type of zinc-binding motif. The electrostatic profile on the surface suggested that a continuous region, including all the conserved basic residues, is involved in the DNA binding, the mode of which is likely to be novel as well.


    Organizational Affiliation

    Age Dimension Research Center, National Insitute of Advanced Industrial Science and Technology, Tsukuba, Japan. k-yamasaki@aist.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
squamosa promoter binding protein-like 7
A
88Arabidopsis thalianaMutation(s): 0 
Gene Names: SPL7
Find proteins for Q8S9G8 (Arabidopsis thaliana)
Go to UniProtKB:  Q8S9G8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations, structures with the lowest energy 
  • Olderado: 1UL5 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance