9S9A | pdb_00009s9a

Crystal structure of the BRL3 ectodomain from Arabidopsis thaliana in complex with 6-deoxocastasterone.

PDB DOI: https://doi.org/10.2210/pdb9S9A/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: 3.20 Å
R-Value Free:
0.280 (Depositor), 0.279 (DCC)
R-Value Work:
0.221 (Depositor), 0.222 (DCC)
R-Value Observed:
0.224 (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: 178.83 kDa
Atom Count: 11,640
Modeled Residue Count: 1,448
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, E, F, G, H C, E, F, G, H, I, J, M, N, O, P	2		N-Glycosylation	Interactions Focus chain C Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain C Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Focus chain M Focus chain N Focus chain O Focus chain P
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-(1-3)-[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	D	10		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G89864BN GlyCosmos: G89864BN GlyGen: G89864BN

Entity ID: 4
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	K	11		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K
Glycosylation Resources
GlyTouCan: G60230HH GlyCosmos: G60230HH GlyGen: G60230HH

Entity ID: 5
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	L	3		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JMI Query on A1JMI Download:Ideal Coordinates CCD File SDF format, chain V [auth B] SDF format, chain Q [auth A] MOL2 format, chain V [auth B] MOL2 format, chain Q [auth A] mmCIF format, chain V [auth B] mmCIF format, chain Q [auth A]	Q [auth A], V [auth B]	6-deoxocastasterone C₂₈ H₅₀ O₄ VXBLCLVRWCLEOX-BFYSZXNBSA-N		Interactions Focus chain Q [auth A] Focus chain V [auth B] Interactions & Density Focus chain Q [auth A] Focus chain V [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] MOL2 format, chain U [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] mmCIF format, chain U [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A]	R [auth A] S [auth A] T [auth A] U [auth A] W [auth B] R [auth A], S [auth A], T [auth A], U [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.280 (Depositor), 0.279 (DCC)
R-Value Work: 0.221 (Depositor), 0.222 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.163	α = 107.015
b = 82.688	β = 91.353
c = 122.196	γ = 112.46

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	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, Database references, Derived calculations, Refinement description, Structure summary