Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 41.53 kDa 
• Atom Count: 3,179 
• Modelled Residue Count: 362 
• Deposited Residue Count: 375 
• Unique protein chains: 1

 5HYZ

Crystal Structure of SCL7 in Oryza sativa

• PDB DOI: 10.2210/pdb5HYZ/pdb

• Classification: TRANSCRIPTION FACTOR
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-02 Released: 2016-04-27 
• Deposition Author(s): Wu, Y., Li, S., Zhao, Y., Sun, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Literature

Crystal Structure of the GRAS Domain of SCARECROW-LIKE7 in Oryza sativa.

Li, S., Zhao, Y., Zhao, Z., Wu, X., Sun, L., Liu, Q., Wu, Y.

(2016) Plant Cell 28: 1025-1034

• PubMed: 27081181 
• DOI: 10.1105/tpc.16.00018
• Primary Citation of Related Structures:  
  5HYZ


• PubMed Abstract: 
  

GRAS proteins belong to a plant-specific protein family with many members and play essential roles in plant growth and development, functioning primarily in transcriptional regulation. Proteins in the family are minimally defined as containing the conserved GRAS domain. Here, we determined the structure of the GRAS domain of Os-SCL7 from rice (Oryza sativa) to 1.82 Å. The structure includes cap and core subdomains and elucidates the features of the conserved GRAS LRI, VHIID, LRII, PFYRE, and SAW motifs. The structure is a dimer, with a clear groove to accommodate double-stranded DNA. Docking a DNA segment into the groove to generate an Os-SCL7/DNA complex provides insight into the DNA binding mechanism of GRAS proteins. Furthermore, the in vitro DNA binding property of Os-SCL7 and model-defined recognition residues are assessed by electrophoretic mobility shift analysis and mutagenesis assays. These studies reveal the structure and preliminary DNA interaction mechanisms of GRAS proteins and open the door to in-depth investigation and understanding of the individual pathways in which they play important roles.

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Organizational Affiliation: 

State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GRAS family transcription factor containing protein, expressed	A	375	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: Os03g0723000, LOC_Os03g51330, OSNPB_030723000, SCL7
UniProt
Find proteins for Q53K16 (Oryza sativa subsp. japonica) Explore Q53K16  Go to UniProtKB:  Q53K16

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.211 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.188	α = 90
b = 179.054	β = 90
c = 59.694	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Wu, Y., Li, S., Zhao, Y., Sun, L.

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2016-06-29
  Changes: Database references