4LSX | pdb_00004lsx

Plant steroid receptor ectodomain bound to brassinolide and SERK1 co-receptor ectodomain

PDB DOI: https://doi.org/10.2210/pdb4LSX/pdb

Classification: STEROID BINDING PROTEIN/PROTEIN BINDING
Organism(s): Arabidopsis thaliana
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2013-07-23 Released: 2013-09-04
Deposition Author(s): Santiago, J., Henzler, C., Hothorn, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free:
0.285 (Depositor), 0.281 (DCC)
R-Value Work:
0.246 (Depositor), 0.241 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Molecular mechanism for plant steroid receptor activation by somatic embryogenesis co-receptor kinases.

Santiago, J., Henzler, C., Hothorn, M.

(2013) Science 341: 889-892

PubMed: 23929946 Search on PubMed
DOI: https://doi.org/10.1126/science.1242468
Primary Citation Related Structures:
4LSA, 4LSC, 4LSX

PubMed Abstract:
Brassinosteroids, which control plant growth and development, are sensed by the leucine-rich repeat (LRR) domain of the membrane receptor kinase BRASSINOSTEROID INSENSITIVE 1 (BRI1), but it is unknown how steroid binding at the cell surface activates the cytoplasmic kinase domain of the receptor. A family of somatic embryogenesis receptor kinases (SERKs) has been genetically implicated in mediating early brassinosteroid signaling events. We found a direct and steroid-dependent interaction between the BRI1 and SERK1 LRR domains by analysis of their complex crystal structure at 3.3 angstrom resolution. We show that the SERK1 LRR domain is involved in steroid sensing and, through receptor-co-receptor heteromerization, in the activation of the BRI1 signaling pathway. Our work reveals how known missense mutations in BRI1 and in SERKs modulate brassinosteroid signaling and the targeting mechanism of BRI1 receptor antagonists.

Organizational Affiliation

Structural Plant Biology Lab, Friedrich Miescher Laboratory of the Max Planck Society, Spemannstraße 39, Tübingen 72076, Germany.

Macromolecule Content

Total Structure Weight: 218.28 kDa
Atom Count: 13,920
Modeled Residue Count: 1,820
Deposited Residue Count: 1,954
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein BRASSINOSTEROID INSENSITIVE 1	A, B	774	Arabidopsis thaliana	Mutation(s): 1 Gene Names: At4g39400, BRI1, F23K16.30 EC: 2.7.11.1 (UniProt), 2.7.10.1 (UniProt)
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: 5	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Somatic embryogenesis receptor kinase 1	C, D	203	Arabidopsis thaliana	Mutation(s): 0 Gene Names: At1g71830, F14O23.21, F14O23_24, SERK1 EC: 2.7.11.1 (UniProt), 2.7.10.1 (UniProt)
UniProt
Find proteins for Q94AG2 (Arabidopsis thaliana) Explore Q94AG2 Go to UniProtKB: Q94AG2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q94AG2
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 3
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	E, H, J	4		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain J Interactions & Density Focus chain E Focus chain H Focus chain J
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, K	2		N-Glycosylation	Interactions Focus chain F Focus chain K Interactions & Density Focus chain F Focus chain K
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	5		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G96947LY GlyCosmos: G96947LY GlyGen: G96947LY

Entity ID: 6
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	I	3		N-Glycosylation	Interactions Focus chain I Interactions & Density Focus chain I
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLD Query on BLD Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B]	L [auth A], O [auth B]	Brassinolide C₂₈ H₄₈ O₆ IXVMHGVQKLDRKH-KNBKMWSGSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Interactions & Density Focus chain L [auth A] Focus chain O [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A] N [auth A] P [auth B] Q [auth C] R [auth C] M [auth A], N [auth A], P [auth B], Q [auth C], R [auth C], S [auth D], T [auth D]	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 P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.30 Å
R-Value Free: 0.285 (Depositor), 0.281 (DCC)
R-Value Work: 0.246 (Depositor), 0.241 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.896	α = 90
b = 69.896	β = 90
c = 873.547	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-09-04

Deposition Author(s):

Santiago, J.

Henzler, C.

Hothorn, M.

Revision History (Full details and data files)

Version 1.0: 2013-09-04
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary