6RY3 | pdb_00006ry3

Structure of the WUS homeodomain

• PDB DOI: https://doi.org/10.2210/pdb6RY3/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-06-10 Released: 2020-04-29 
• Deposition Author(s): Sloan, J.J., Wild, K., Sinning, I.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.213 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Structural basis for the complex DNA binding behavior of the plant stem cell regulator WUSCHEL.

Sloan, J., Hakenjos, J.P., Gebert, M., Ermakova, O., Gumiero, A., Stier, G., Wild, K., Sinning, I., Lohmann, J.U.

(2020) Nat Commun 11: 2223-2223

• PubMed: 32376862 
• DOI: https://doi.org/10.1038/s41467-020-16024-y
• Primary Citation Related Structures: 
  6RY3, 6RYD, 6RYI, 6RYL


• PubMed Abstract: 
  

  Stem cells are one of the foundational evolutionary novelties that allowed the independent emergence of multicellularity in the plant and animal lineages. In plants, the homeodomain (HD) transcription factor WUSCHEL (WUS) is essential for the maintenance of stem cells in the shoot apical meristem. WUS has been reported to bind to diverse DNA motifs and to act as transcriptional activator and repressor. However, the mechanisms underlying this remarkable behavior have remained unclear. Here, we quantitatively delineate WUS binding to three divergent DNA motifs and resolve the relevant structural underpinnings. We show that WUS exhibits a strong binding preference for TGAA repeat sequences, while retaining the ability to weakly bind to TAAT elements. This behavior is attributable to the formation of dimers through interactions of specific residues in the HD that stabilize WUS DNA interaction. Our results provide a mechanistic basis for dissecting WUS dependent regulatory networks in plant stem cell control.

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Organizational Affiliation: 
• Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
BASF SE, Carl-Bosch-Strasse 38, 67056, Ludwigshafen am Rhein, Germany.
Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
Celonic AG, Eulerstrasse 55, 4051, Basel, Switzerland.
Instituto Poligrafico e Zecca dello Stato S.p.A., Via Salaria, I-712-00138, Roma, Italy.
Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany. [e-mail].
Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 9.18 kDa 
• Atom Count: 641 
• Modeled Residue Count: 65 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein WUSCHEL	A	76	Arabidopsis thaliana	Mutation(s): 0  Gene Names: WUS, PGA6, At2g17950, T27K22.18
UniProt
Find proteins for Q9SB92 (Arabidopsis thaliana) Explore Q9SB92  Go to UniProtKB:  Q9SB92

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACE	C [auth A], D [auth A], E [auth A]	ACETYL GROUP C2 H4 O IKHGUXGNUITLKF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.213 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.12	α = 90
b = 43.12	β = 90
c = 82.01	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-04-29 
Deposition Author(s): Sloan, J.J., Wild, K., Sinning, I.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History  

• Version 1.0: 2020-04-29
  Type: Initial release
  
• Version 1.1: 2020-05-20
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description