9S90 | pdb_00009s90

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

PDB DOI: https://doi.org/10.2210/pdb9S90/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-08-05 Released: 2025-09-03
Deposition Author(s): Caregnato, A., Hothorn, M.
Funding Organization(s): Swiss National Science Foundation

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

Ligand Structure Quality Assessment

This is version 1.0 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.

To be published.

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

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-like protein kinase BRI1-like 3	A, B	779	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BRL3, At3g13380, MRP15.1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9LJF3
Glycosylation
Glycosylation Sites: 11	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain G Focus chain I Focus chain J Focus chain K Focus chain L Focus chain O Focus chain Q Focus chain R Interactions & Density Focus chain C Focus chain D Focus chain G Focus chain I Focus chain J Focus chain K Focus chain L Focus chain O Focus chain Q Focus chain R
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	11		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G60230HH GlyCosmos: G60230HH GlyGen: G60230HH

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, N	3		N-Glycosylation	Interactions Focus chain F Focus chain N Interactions & Density Focus chain F Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H, P	3		N-Glycosylation	Interactions Focus chain H Focus chain P Interactions & Density Focus chain H Focus chain P
Glycosylation Resources
GlyTouCan: G94817IN GlyCosmos: G94817IN GlyGen: G94817IN

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	10		N-Glycosylation	Interactions Focus chain M Interactions & Density Focus chain M
Glycosylation Resources
GlyTouCan: G89864BN GlyCosmos: G89864BN GlyGen: G89864BN

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JME Query on A1JME Download:Ideal Coordinates CCD File SDF format, chain X [auth B] SDF format, chain S [auth A] MOL2 format, chain X [auth B] MOL2 format, chain S [auth A] mmCIF format, chain X [auth B] mmCIF format, chain S [auth A]	S [auth A], X [auth B]	Castasterone C₂₈ H₄₈ O₅ VYUIKSFYFRVQLF-YLNAYWRASA-N		Interactions Focus chain S [auth A] Focus chain X [auth B] Interactions & Density Focus chain S [auth A] Focus chain X [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain AA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain AA [auth B]	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		Interactions Focus chain AA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain T [auth A] Focus chain U [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain FA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B]	CA [auth B], DA [auth B], FA [auth B], V [auth A], W [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth B] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain FA [auth B] Focus chain V [auth A] Focus chain W [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain BA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain BA [auth B]	BA [auth B], EA [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BA [auth B] Focus chain EA [auth B] Interactions & Density Focus chain BA [auth B] Focus chain EA [auth B]