3T4L

Arabidopsis histidine kinase 4 sensor domain in complex with trans-zeatin

• PDB DOI: https://doi.org/10.2210/pdb3T4L/pdb

• Classification: hormone receptor
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-26 Released: 2011-10-05 
• Deposition Author(s): Hothorn, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.200 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Structural basis for cytokinin recognition by Arabidopsis thaliana histidine kinase 4.

Hothorn, M., Dabi, T., Chory, J.

(2011) Nat Chem Biol 7: 766-768

• PubMed: 21964459 
• DOI: https://doi.org/10.1038/nchembio.667
• Primary Citation of Related Structures:  
  3T4J, 3T4K, 3T4L, 3T4O, 3T4Q, 3T4S, 3T4T


• PubMed Abstract: 
  

  Cytokinins are classic hormones that orchestrate plant growth and development and the integrity of stem cell populations. Cytokinin receptors are eukaryotic sensor histidine kinases that are activated by both naturally occurring adenine-type cytokinins and urea-based synthetic compounds. Crystal structures of the Arabidopsis thaliana histidine kinase 4 sensor domain in complex with different cytokinin ligands now rationalize the hormone-binding specificity of the receptor and may spur the design of new cytokinin ligands.

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Organizational Affiliation: 

Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 62.01 kDa 
• Atom Count: 5,035 
• Modelled Residue Count: 529 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histidine kinase 4	A, B	270	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AHK4, At2g01830, CRE1, RAW1, T23K3.2, WOL 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZEA	C [auth A], E [auth B]	(2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol C10 H13 N5 O UZKQTCBAMSWPJD-FARCUNLSSA-N
MLI	D [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
ZEA	BindingDB:  3T4L	EC50: 1100 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 0.200 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.79	α = 90
b = 59.79	β = 90
c = 297.28	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Hothorn, M.

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2011-12-14
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary