5B3G

The crystal structure of the heterodimer of SHORT-ROOT and SCARECROW GRAS domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD

Hirano, Y.Nakagawa, M.Suyama, T.Murase, K.Shirakawa, M.Takayama, S.Sun, T.P.Hakoshima, T.

(2017) Nat Plants 3: 17010-17010

  • DOI: https://doi.org/10.1038/nplants.2017.10
  • Primary Citation of Related Structures:  
    5B3G, 5B3H

  • PubMed Abstract: 

    The plant-specific GAI, RGA and SCR (GRAS) family proteins play critical roles in plant development and signalling. Two GRAS proteins, SHORT-ROOT (SHR) and SCARECROW (SCR), cooperatively direct asymmetric cell division and the patterning of root cell types by transcriptional control in conjunction with BIRD/INDETERMINATE DOMAIN (IDD) transcription factors, although precise details of these specific interactions and actions remain unknown. Here, we present the crystal structures of the SHR-SCR binary and JACKDAW (JKD)/IDD10-SHR-SCR ternary complexes. Each GRAS domain comprises one α/β core subdomain with an α-helical cap that mediates heterodimerization by forming an intermolecular helix bundle. The α/β core subdomain of SHR forms the BIRD binding groove, which specifically recognizes the zinc fingers of JKD. We identified a conserved SHR-binding motif in 13 BIRD/IDD transcription factors. Our results establish a structural basis for GRAS-GRAS and GRAS-BIRD interactions and provide valuable clues towards our understanding of these regulators, which are involved in plant-specific signalling networks.


  • Organizational Affiliation

    Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SCARECROW382Arabidopsis thalianaMutation(s): 0 
Gene Names: SCRSGR1At3g54220F24B22.180
UniProt
Find proteins for Q9M384 (Arabidopsis thaliana)
Explore Q9M384 
Go to UniProtKB:  Q9M384
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M384
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SHORT-ROOT475Arabidopsis thalianaMutation(s): 0 
Gene Names: SHRSGR7At4g37650F19F18.140
UniProt
Find proteins for Q9SZF7 (Arabidopsis thaliana)
Explore Q9SZF7 
Go to UniProtKB:  Q9SZF7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SZF7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.7α = 90
b = 84.428β = 92.66
c = 89.797γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and TechnologyJapan25440025
Ministry of Education, Culture, Sports, Science and TechnologyJapan22121002

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection