1UL4

Solution structure of the DNA-binding domain of squamosa promoter binding protein-like 4


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 1.4 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: https://doi.org/10.1016/j.jmb.2004.01.015
  • Primary Citation of Related Structures:  
    1UL4, 1UL5

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
squamosa promoter binding protein-like 494Arabidopsis thalianaMutation(s): 0 
Gene Names: SPL4
UniProt
Find proteins for Q9S7A9 (Arabidopsis thaliana)
Explore Q9S7A9 
Go to UniProtKB:  Q9S7A9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S7A9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
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 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-09
    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: 2022-03-02
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection