4LSC | pdb_00004lsc

Isolated SERK1 co-receptor ectodomain at high resolution

• PDB DOI: https://doi.org/10.2210/pdb4LSC/pdb

• Classification: PROTEIN BINDING
• Organism(s): Arabidopsis thaliana
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2013-07-22 Released: 2013-09-04 
• Deposition Author(s): Santiago, J., Henzler, C., Hothorn, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.53 Å
• R-Value Free: 
  0.177 (Depositor), 0.181 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Molecular mechanism for plant steroid receptor activation by somatic embryogenesis co-receptor kinases.

Santiago, J., Henzler, C., Hothorn, M.

(2013) Science 341: 889-892

• PubMed: 23929946 
• DOI: https://doi.org/10.1126/science.1242468
• Primary Citation Related Structures: 
  4LSA, 4LSC, 4LSX


• PubMed Abstract: 
  

  Brassinosteroids, which control plant growth and development, are sensed by the leucine-rich repeat (LRR) domain of the membrane receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1), but it is unknown how steroid binding at the cell surface activates the cytoplasmic kinase domain of the receptor. A family of somatic embryogenesis receptor kinases (SERKs) has been genetically implicated in mediating early brassinosteroid signaling events. We found a direct and steroid-dependent interaction between the BRI1 and SERK1 LRR domains by analysis of their complex crystal structure at 3.3 angstrom resolution. We show that the SERK1 LRR domain is involved in steroid sensing and, through receptor-co-receptor heteromerization, in the activation of the BRI1 signaling pathway. Our work reveals how known missense mutations in BRI1 and in SERKs modulate brassinosteroid signaling and the targeting mechanism of BRI1 receptor antagonists.

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Organizational Affiliation: 
• Structural Plant Biology Lab, Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 25.56 kDa 
• Atom Count: 1,673 
• Modeled Residue Count: 186 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Somatic embryogenesis receptor kinase 1	A	223	Arabidopsis thaliana	Mutation(s): 2  Gene Names: At1g71830, F14O23.21, F14O23_24, SERK1 EC: 2.7.11.1 (UniProt), 2.7.10.1 (UniProt)
UniProt
Find proteins for Q94AG2 (Arabidopsis thaliana) Explore Q94AG2  Go to UniProtKB:  Q94AG2
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G32152BH GlyCosmos: G32152BH GlyGen: G32152BH

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [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: 1.53 Å
• R-Value Free:  0.177 (Depositor), 0.181 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.63	α = 90
b = 72.63	β = 90
c = 80.97	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Santiago, J., Henzler, C., Hothorn, M.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary