8WEB

Crystal structure of Arabidopsis thaliana MIK2 ectodomain

• PDB DOI: https://doi.org/10.2210/pdb8WEB/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-09-17 Released: 2024-11-06 
• Deposition Author(s): Wan, L.H., Hu, Y.X., Wu, H.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.201 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Starting Model: in silico

Literature

Mechanistic study of SCOOPs recognition by MIK2-BAK1 complex reveals the role of N-glycans in plant ligand-receptor-coreceptor complex formation

Hu, Y.X., Wu, H.M.

(2024) Nature Plants 

• DOI: https://doi.org/10.1038/s41477-024-01836-3

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 82.51 kDa 
• Atom Count: 5,909 
• Modelled Residue Count: 646 
• Deposited Residue Count: 712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MDIS1-interacting receptor like kinase 2	A	712	Arabidopsis thaliana	Mutation(s): 3  Gene Names: MIK2, At4g08850, T32A17.160 EC: 2.7.11.1
UniProt
Find proteins for Q8VZG8 (Arabidopsis thaliana) Explore Q8VZG8  Go to UniProtKB:  Q8VZG8
Glycosylation
Glycosylation Sites: 11

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D, E, F, G	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.201 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.127	α = 90
b = 107.889	β = 90
c = 164.305	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-06 
Deposition Author(s): Wan, L.H., Hu, Y.X., Wu, H.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32000900

Revision History  

• Version 1.0: 2024-11-06
  Type: Initial release