Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 28.21 kDa 
• Atom Count: 1811 
• Modelled Residue Count: 215 
• Deposited Residue Count: 262 
• Unique protein chains: 1

5LY0

Crystal structure of LOB domain of Ramosa2 from Wheat

• PDB DOI: 10.2210/pdb5LY0/pdb

• Classification: TRANSCRIPTION
• Organism(s): Triticum turgidum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-23 Released: 2017-10-25 
• Deposition Author(s): Wei, X.-B., Zhang, B., Chen, W.-F., Fan, S.-H., Rety, S., Xi, X.-G.
• Funding Organization(s): National Natural Science Foundation, Northwest A University Startup Funding

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.231 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Literature

Structural analysis reveals a "molecular calipers" mechanism for a LATERAL ORGAN BOUNDARIES DOMAIN transcription factor protein from wheat.

Chen, W.F., Wei, X.B., Rety, S., Huang, L.Y., Liu, N.N., Dou, S.X., Xi, X.G.

(2019) J Biol Chem 294: 142-156

• PubMed: 30425099 
• DOI: 10.1074/jbc.RA118.003956
• Primary Citation of Related Structures:  
  5LY0


• PubMed Abstract: 
  

LATERAL ORGAN BOUNDARIES DOMAIN (LBD) proteins, a family of plant-specific transcription factors harboring a conserved Lateral Organ Boundaries (LOB) domain, are regulators of plant organ development. Recent studies have unraveled additional pivotal roles of the LBD protein family beyond defining lateral organ boundaries, such as pollen development and nitrogen metabolism. The structural basis for the molecular network of LBD-dependent processes remains to be deciphered. Here, we solved the first structure of the homodimeric LOB domain of Ramosa2 from wheat (TtRa2LD) to 1.9 Å resolution. Our crystal structure reveals structural features shared with other zinc-finger transcriptional factors, as well as some features unique to LBD proteins. Formation of the TtRa2LD homodimer relied on hydrophobic interactions of its coiled-coil motifs. Several specific motifs/domains of the LBD protein were also involved in maintaining its overall conformation. The intricate assembly within and between the monomers determined the precise spatial configuration of the two zinc fingers that recognize palindromic DNA sequences. Biochemical, molecular modeling, and small-angle X-ray scattering experiments indicated that dimerization is important for cooperative DNA binding and discrimination of palindromic DNA through a molecular calipers mechanism. Along with previously published data, this study enables us to establish an atomic-scale mechanistic model for LBD proteins as transcriptional regulators in plants.

---

Organizational Affiliation: 

the LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61 Avenue du Président Wilson, F-94235 Cachan, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LOB family transfactor Ramosa2.1	A, B	131	Triticum turgidum	Mutation(s): 0
UniProt
Find proteins for D9MPF3 (Triticum turgidum subsp. durum) Explore D9MPF3  Go to UniProtKB:  D9MPF3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.231 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.345	α = 90
b = 85.206	β = 90
c = 93.334	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
autoSHARP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-09-23 
• Released Date: 2017-10-25 
Deposition Author(s): Wei, X.-B., Zhang, B., Chen, W.-F., Fan, S.-H., Rety, S., Xi, X.-G.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation	China	31370798, 11304252, 31301632
Northwest A University Startup Funding	China	Z101021102

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Database references
• Version 1.2: 2019-02-27
  Changes: Data collection, Database references