9S90 | pdb_00009s90

Crystal structure of the BRL3 ectodomain from Arabidopsis thaliana in complex with castasterone.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 
    0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

A mechanistic framework for the recognition of chemically diverse brassinosteroids by BRI1-family receptor kinases.

Caregnato, A.Chen, H.Kvasnica, M.Hohmann, U.Oklestkova, J.Ferrer, K.Broger, L.Hothorn, L.A.Strnad, M.Hothorn, M.

(2026) Nat Plants 

  • DOI: https://doi.org/10.1038/s41477-026-02346-0
  • Primary Citation Related Structures: 
    9S80, 9S87, 9S8S, 9S8V, 9S8Z, 9S90, 9S96, 9S9A, 9S9C, 9U0G

  • PubMed Abstract: 

    Brassinosteroids (BRs) are chemically diverse plant steroid hormones produced via a branched biosynthetic pathway. The potent BR brassinolide is sensed by the membrane receptor kinase BRI1 and a SERK co-receptor, but the physiological functions of other abundant BRs remain to be characterized. Here we present quantitative binding kinetics for 4 Arabidopsis thaliana BR receptors and 15 BRs, which define the key chemical features required for high-affinity receptor binding, ligand positioning and co-receptor recognition. BRI1, BRL1 and BRL3 share overlapping ligand preferences, whereas BRL2 binds C 28 BRs with moderate affinity. Structural analyses of BR-bound BRI1 and BRL3 ectodomains combined with extensive in vitro and in vivo mutagenesis studies reveal a high structural plasticity of the hormone-binding pocket. Functional assays using structure-based BR agonists and antagonists uncover that BR receptor-co-receptor signalling complexes can recognize chemically diverse BRs, introducing an additional, intriguing layer of BR signalling regulation.


  • Organizational Affiliation
    • Structural Plant Biology Laboratory, Department of Plant Sciences, University of Geneva, Geneva, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 180.07 kDa 
  • Atom Count: 11,674 
  • Modeled Residue Count: 1,446 
  • Deposited Residue Count: 1,558 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-like protein kinase BRI1-like 3
A, B
779Arabidopsis thalianaMutation(s): 0 
Gene Names: BRL3At3g13380MRP15.1
EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for Q9LJF3 (Arabidopsis thaliana)
Explore Q9LJF3 
Go to UniProtKB:  Q9LJF3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LJF3
Glycosylation
Glycosylation Sites: 11
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D, G, I, J
C, D, G, I, J, K, L, O, Q, R
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
11N-Glycosylation
Glycosylation Resources
GlyTouCan: G60230HH
GlyCosmos: G60230HH
GlyGen: G60230HH
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F, N
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
H, P
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G94817IN
GlyCosmos: G94817IN
GlyGen: G94817IN
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M
10N-Glycosylation
Glycosylation Resources
GlyTouCan: G89864BN
GlyCosmos: G89864BN
GlyGen: G89864BN

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1JME

Query on A1JME



Download:Ideal Coordinates CCD File
S [auth A],
X [auth B]
Castasterone
C28 H48 O5
VYUIKSFYFRVQLF-YLNAYWRASA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B],
T [auth A],
U [auth A],
Y [auth B],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
CA [auth B],
DA [auth B],
FA [auth B],
V [auth A],
W [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT



Download:Ideal Coordinates CCD File
BA [auth B],
EA [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free:  0.258 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.226 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.257α = 107.022
b = 81.94β = 91.499
c = 122.476γ = 112.53
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030_205201

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2026-08-12
    Changes: Database references
  • Version 1.2: 2026-08-19
    Changes: Database references