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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.00 kDa 
• Atom Count: 2272 
• Modelled Residue Count: 266 
• Deposited Residue Count: 286 
• Unique protein chains: 1

7P8D

Crystal structure of the Receiver domain of A. thaliana cytokinin receptor AtCRE1 in complex with Mg2+

• PDB DOI: 10.2210/pdb7P8D/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-07-21 Released: 2021-10-20 
• Deposition Author(s): Tran, L.H., Urbanowicz, A., Jasinski, M., Jaskolski, M., Ruszkowski, M.
• Funding Organization(s): Polish National Science Centre

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.246 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From Arabidopsis thaliana and Medicago truncatula .

Tran, L.H., Urbanowicz, A., Jasinski, M., Jaskolski, M., Ruszkowski, M.

(2021) Front Plant Sci 12: 756341-756341

• PubMed: 34630499 
• DOI: 10.3389/fpls.2021.756341
• Primary Citation of Related Structures:  
  7P8C, 7P8D, 7P8E


• PubMed Abstract: 
  

Cytokinins are phytohormones regulating many biological processes that are vital to plants. CYTOKININ RESPONSE1 (CRE1), the main cytokinin receptor, has a modular architecture composed of a cytokinin-binding CHASE (Cyclases/Histidine kinases Associated Sensory Extracellular) domain, followed by a transmembrane fragment, an intracellular histidine kinase (HK) domain, and a receiver domain (REC). Perception of cytokinin signaling involves (i) a hormone molecule binding to the CHASE domain, (ii) CRE1 autophosphorylation at a conserved His residue in the HK domain, followed by a phosphorelay to (iii) a conserved Asp residue in the REC domain, (iv) a histidine-containing phosphotransfer protein (HPt), and (v) a response regulator (RR). This work focuses on the crystal structures of the REC domain of CRE1 from the model plant Arabidopsis thaliana and from the model legume Medicago truncatula . Both REC domains form tight 3D-domain-swapped dimers. Dimerization of the REC domain agrees with the quaternary assembly of the entire CRE1 but is incompatible with a model of its complex with HPt, suggesting that a considerable conformational change should occur to enable the signal transduction. Indeed, phosphorylation of the REC domain can change the HPt-binding properties of CRE1, as shown by functional studies.

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Organizational Affiliation: 

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receiver domain of histidine kinase 4	A, B	143	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AHK4, CRE1, RAW1, WOL, At2g01830, T23K3.2 EC: 2.7.13.3 (PDB Primary Data), 3.1.3.16 (PDB Primary Data)
UniProt
Find proteins for Q9C5U0 (Arabidopsis thaliana) Explore Q9C5U0  Go to UniProtKB:  Q9C5U0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
EDO	E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.246 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data DOI: 10.18150/UUYPCU Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.183	α = 90
b = 99.202	β = 90
c = 35.623	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2021-07-21 
• Released Date: 2021-10-20 
Deposition Author(s): Tran, L.H., Urbanowicz, A., Jasinski, M., Jaskolski, M., Ruszkowski, M.

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Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	SONATA 2018/31/D/NZ1/03630

Revision History  

• Version 1.0: 2021-10-20
  Type: Initial release
  
• Version 1.1: 2022-02-02
  Changes: Structure summary