9S96 | pdb_00009s96

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

PDB DOI: https://doi.org/10.2210/pdb9S96/pdb

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

Deposited: 2025-08-06 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: 2.31 Å
R-Value Free:
0.239 (Depositor), 0.240 (DCC)
R-Value Work:
0.215 (Depositor), 0.217 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 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: 180.77 kDa
Atom Count: 11,885
Modeled Residue Count: 1,435
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: 10	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, F, G, H C, D, F, G, H, J, K, L, M, P, Q, S	2		N-Glycosylation	Interactions Focus chain C Focus chain D Focus chain F Focus chain G Focus chain H Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain Q Focus chain S Interactions & Density Focus chain C Focus chain D Focus chain F Focus chain G Focus chain H Focus chain J Focus chain K Focus chain L Focus chain M Focus chain P Focus chain Q Focus chain S
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
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	I, R	3		N-Glycosylation	Interactions Focus chain I Focus chain R Interactions & Density Focus chain I Focus chain R
Glycosylation Resources
GlyTouCan: G94817IN GlyCosmos: G94817IN GlyGen: G94817IN

Entity ID: 5
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-(1-6)-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	N	9		N-Glycosylation	Interactions Focus chain N Interactions & Density Focus chain N
Glycosylation Resources
GlyTouCan: G04414GO GlyCosmos: G04414GO GlyGen: G04414GO

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	O	2		N/A	Interactions Focus chain O Interactions & Density Focus chain O
Glycosylation Resources
GlyTouCan: G53402KW GlyCosmos: G53402KW GlyGen: G53402KW

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	T	3		N-Glycosylation	Interactions Focus chain T Interactions & Density Focus chain T
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JMF Query on A1JMF Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain U [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain U [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain U [auth A]	CA [auth B], U [auth A]	Typhasterol C₂₈ H₄₈ O₄ SBSXXCCMIWEPEE-SELDZKRUSA-N		Interactions Focus chain CA [auth B] Focus chain U [auth A] Interactions & Density Focus chain CA [auth B] Focus chain U [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain EA [auth B]	DA [auth B], EA [auth B], V [auth A], W [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain V [auth A] Focus chain W [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain JA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain JA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain JA [auth B]	JA [auth B], Z [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain JA [auth B] Focus chain Z [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain FA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain GA [auth B] SDF format, chain BA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain BA [auth B]	AA [auth A] BA [auth B] FA [auth B] GA [auth B] HA [auth B] AA [auth A], BA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], X [auth A], Y [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain X [auth A] Focus chain Y [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] MOL2 format, chain KA [auth B] mmCIF format, chain KA [auth B]	KA [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain KA [auth B] Interactions & Density Focus chain KA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.31 Å
R-Value Free: 0.239 (Depositor), 0.240 (DCC)
R-Value Work: 0.215 (Depositor), 0.217 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.267	α = 106.963
b = 81.848	β = 91.77
c = 122.382	γ = 112.835

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Caregnato, A.

Hothorn, M.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	310030_205201

Revision History (Full details and data files)

Version 1.0: 2025-09-03
Type: Initial release
Version 2.0: 2026-02-18
Type: Coordinate replacement
Reason: Chirality error
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Refinement description, Structure summary