Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 67.38 kDa 
• Atom Count: 3246 
• Modelled Residue Count: 365 
• Deposited Residue Count: 600 
• Unique protein chains: 1

6R1H

Crystal structure of the LRR ectodomain of the receptor kinase SOBIR1 from Arabidopsis thaliana.

• PDB DOI: 10.2210/pdb6R1H/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Arabidopsis thaliana
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2019-03-14 Released: 2019-05-08 
• Deposition Author(s): Hohmann, U., Hothorn, M.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.188 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 

Literature

Crystal structure of the leucine-rich repeat ectodomain of the plant immune receptor kinase SOBIR1.

Hohmann, U., Hothorn, M.

(2019) Acta Crystallogr D Struct Biol 75: 488-497

• PubMed: 31063151 
• DOI: 10.1107/S2059798319005291
• Primary Citation of Related Structures:  
  6R1H


• PubMed Abstract: 
  

Plant-unique membrane receptor kinases with leucine-rich repeat (LRR) extracellular domains are key regulators of development and immune responses. Here, the 1.55 Å resolution crystal structure of the immune receptor kinase SOBIR1 from Arabidopsis is presented. The ectodomain structure reveals the presence of five LRRs sandwiched between noncanonical capping domains. The disulfide-bond-stabilized N-terminal cap harbours an unusual β-hairpin structure. The C-terminal cap features a highly positively charged linear motif which was found to be largely disordered in this structure. Size-exclusion chromatography and right-angle light-scattering experiments suggest that SOBIR1 is a monomer in solution. The protruding β-hairpin, a set of highly conserved basic residues at the inner surface of the SOBIR LRR domain and the presence of a genetic missense allele in LRR2 together suggest that the SOBIR1 ectodomain may mediate protein-protein interaction in plant immune signalling.

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Organizational Affiliation: 

Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat receptor-like serine/threonine/tyrosine-protein kinase SOBIR1	A, B	300	Arabidopsis thaliana	Mutation(s): 0  Gene Names: SOBIR1, EVR, At2g31880, F20M17.8 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q9SKB2 (Arabidopsis thaliana) Explore Q9SKB2  Go to UniProtKB:  Q9SKB2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.188 
• R-Value Work: 0.172 
• R-Value Observed: 0.173 
• Space Group: P 6₅
• Diffraction Data DOI: 10.5281/zenodo.2595891 Protein Diffraction
• Diffraction Data DOI: 10.5281/zenodo.2594485 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.246	α = 90
b = 82.246	β = 90
c = 109.863	γ = 120

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: 2019-03-14 
• Released Date: 2019-05-08 
Deposition Author(s): Hohmann, U., Hothorn, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31CP30_180213

Revision History  

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 1.1: 2019-05-15
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary