9S80 | pdb_00009s80

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

PDB DOI: https://doi.org/10.2210/pdb9S80/pdb

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

Deposited: 2025-08-05 Released: 2025-09-10
Deposition Author(s): Hohmann, U., Hothorn, M.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.258 (Depositor), 0.258 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.223 (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: 179.87 kDa
Atom Count: 12,040
Modeled Residue Count: 1,448
Deposited Residue Count: 1,540
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-like protein kinase BRI1-like 3	A, B	770	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9LJF3
Glycosylation
Glycosylation Sites: 13	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	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E, H, J C, D, E, H, J, K, L, M, P, R, S, T	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain E Focus chain H Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain R Focus chain S Focus chain T Interactions & Density Focus chain C Focus chain D Focus chain E Focus chain H Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain R Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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

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

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLD Query on BLD Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain U [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain U [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain U [auth A]	DA [auth B], U [auth A]	Brassinolide C₂₈ H₄₈ O₆ IXVMHGVQKLDRKH-KNBKMWSGSA-N		Interactions Focus chain DA [auth B] Focus chain U [auth A] Interactions & Density Focus chain DA [auth B] Focus chain U [auth A]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain Z [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain Z [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain Z [auth A]	HA [auth B], Z [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain HA [auth B] Focus chain Z [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	EA [auth B] FA [auth B] GA [auth B] V [auth A] W [auth A] EA [auth B], FA [auth B], GA [auth B], V [auth A], W [auth A], X [auth A], Y [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain KA [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain KA [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain KA [auth B]	BA [auth A], KA [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth A] Focus chain KA [auth B] Interactions & Density Focus chain BA [auth A] Focus chain KA [auth B]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain CA [auth B] MOL2 format, chain CA [auth B] mmCIF format, chain CA [auth B]	CA [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Interactions & Density Focus chain CA [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain IA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain IA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain IA [auth B]	AA [auth A], IA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain IA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain IA [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain JA [auth B] MOL2 format, chain JA [auth B] mmCIF format, chain JA [auth B]	JA [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain JA [auth B] Interactions & Density Focus chain JA [auth B]