9S8Z | pdb_00009s8z

Crystal structure of the BRI1 ectodomain from Arabidopsis thaliana in complex with 28-homobrassinolide.

PDB DOI: https://doi.org/10.2210/pdb9S8Z/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): Caregnato, A., Hothorn, M.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.256 (Depositor), 0.256 (DCC)
R-Value Work:
0.230 (Depositor), 0.230 (DCC)
R-Value Observed:
0.231 (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: 92.74 kDa
Atom Count: 6,076
Modeled Residue Count: 743
Deposited Residue Count: 797
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BRASSINOSTEROID INSENSITIVE 1	A	797	Arabidopsis thaliana	Mutation(s): 0 Gene Names: BRI1, At4g39400, F23K16.30 EC: 2.7.10.1 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for O22476 (Arabidopsis thaliana) Explore O22476 Go to UniProtKB: O22476
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O22476
Glycosylation
Glycosylation Sites: 10	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	B, F	4		N-Glycosylation	Interactions Focus chain B Focus chain F Interactions & Density Focus chain B Focus chain F
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 3
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, H	2		N-Glycosylation	Interactions Focus chain C Focus chain E Focus chain H Interactions & Density Focus chain C Focus chain E Focus chain H
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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	7		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 5
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	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1JMH Query on A1JMH Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	28-Homobrassinolide C₂₉ H₅₀ O₆ HJIKODJJEORHMZ-NNPZUXBVSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A], N [auth A], O [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A]	J [auth A], K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A]	R [auth A], S [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain R [auth A] Focus chain S [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.256 (Depositor), 0.256 (DCC)
R-Value Work: 0.230 (Depositor), 0.230 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.077	α = 90
b = 66.735	β = 121.954
c = 121.604	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	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: 2025-09-10

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: 2025-09-10
Type: Initial release
Version 2.0: 2026-02-18
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary