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- PDB-9s8s: Crystal structure of the BRI1 ectodomain from Arabidopsis thalian... -

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Basic information

Entry
Database: PDB / ID: 9s8s
TitleCrystal structure of the BRI1 ectodomain from Arabidopsis thaliana in complex with typhasterol.
ComponentsProtein BRASSINOSTEROID INSENSITIVE 1
KeywordsMEMBRANE PROTEIN / receptor kinase / steroid receptor / brassinosteroids / leucine-rich repeat
Function / homology
Function and homology information


anther wall tapetum cell differentiation / pollen exine formation / detection of brassinosteroid stimulus / brassinosteroid homeostasis / skotomorphogenesis / positive regulation of flower development / seedling development / leaf development / brassinosteroid mediated signaling pathway / response to water deprivation ...anther wall tapetum cell differentiation / pollen exine formation / detection of brassinosteroid stimulus / brassinosteroid homeostasis / skotomorphogenesis / positive regulation of flower development / seedling development / leaf development / brassinosteroid mediated signaling pathway / response to water deprivation / microtubule bundle formation / response to UV-B / response to light stimulus / steroid binding / hormone-mediated signaling pathway / transmembrane receptor protein tyrosine kinase activity / SNARE binding / receptor protein-tyrosine kinase / signaling receptor activity / protein kinase activity / non-specific serine/threonine protein kinase / endosome membrane / endosome / protein heterodimerization activity / protein serine kinase activity / protein serine/threonine kinase activity / protein homodimerization activity / protein-containing complex / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Brassinosteroid receptor BRI1, island domain / Brassinosteroid receptor island domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily ...Brassinosteroid receptor BRI1, island domain / Brassinosteroid receptor island domain / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Protein BRASSINOSTEROID INSENSITIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å
AuthorsCaregnato, A. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_205201 Switzerland
CitationJournal: To Be Published
Title: A mechanistic framework for the recognition of chemically diverse brassinosteroids by BRI1-family receptor kinases.
Authors: Caregnato, A. / Chen, H. / Kvasnica, M. / Hohmann, U. / Oklestkova, J. / Ferrer, K. / Broger, L. / Hothorn, L.A. / Strnad, M. / Hothorn, M.
History
DepositionAug 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 2.0Feb 18, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_name_com / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] ..._atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity_name_com.name / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entity_branch_link.atom_id_2 / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_link.comp_id_2 / _pdbx_entity_branch_link.entity_branch_list_num_1 / _pdbx_entity_branch_link.entity_branch_list_num_2 / _pdbx_entity_branch_link.entity_id / _pdbx_entity_branch_link.leaving_atom_id_2 / _pdbx_entity_branch_list.comp_id / _pdbx_entity_branch_list.entity_id / _pdbx_entity_branch_list.num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_sheet_range.id / _struct_sheet_range.sheet_id
Description: Chirality error
Details: Dear Curator, Matthew Conroy from LIPID MAPS has informed us that our ligand entry A1JMF (typhasterol) contains a chirality error at position C14. We have generated new ligand restraints and ...Details: Dear Curator, Matthew Conroy from LIPID MAPS has informed us that our ligand entry A1JMF (typhasterol) contains a chirality error at position C14. We have generated new ligand restraints and corrected the error. Best regards, Michael Hothorn
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein BRASSINOSTEROID INSENSITIVE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,50212
Polymers86,4401
Non-polymers4,06211
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)174.173, 66.652, 119.705
Angle α, β, γ (deg.)90.000, 121.665, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-902-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Protein BRASSINOSTEROID INSENSITIVE 1 / AtBRI1 / Brassinosteroid LRR receptor kinase / BRI1 leucine-rich repeat ectodomain


Mass: 86439.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0 / Gene: BRI1, At4g39400, F23K16.30 / Plasmid: pBB2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tnao38
References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Sugars , 5 types, 7 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 68 molecules

#6: Chemical ChemComp-A1JMF / Typhasterol / (3R,5S,8S,9S,10R,13S,14S,17R)-17-[(2S,3R,4R,5S)-5,6-dimethyl-3,4-bis(oxidanyl)heptan-2-yl]-10,13-dimethyl-3-oxidanyl-1,2,3,4,5,7,8,9,11,12,14,15,16,17-tetradecahydrocyclopenta[a]phenanthren-6-one


Mass: 448.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H48O4
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 25% PEG 3350, 0.2 M lithium sulfate, 0.1 M citric acid pH 4.0, 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000009 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000009 Å / Relative weight: 1
ReflectionResolution: 2.65→47.87 Å / Num. obs: 64742 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 85.48 Å2 / CC1/2: 1 / Rrim(I) all: 0.084 / Net I/σ(I): 12.9
Reflection shellResolution: 2.65→2.81 Å / Redundancy: 6.7 % / Num. unique obs: 10560 / CC1/2: 0.458 / Rrim(I) all: 2.381 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.65→47.87 Å / SU ML: 0.553 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.1579
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2752 3239 5 %
Rwork0.248 61503 -
obs0.2494 64742 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.68 Å2
Refinement stepCycle: LAST / Resolution: 2.65→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5621 0 268 64 5953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00385997
X-RAY DIFFRACTIONf_angle_d0.68848145
X-RAY DIFFRACTIONf_chiral_restr0.0415998
X-RAY DIFFRACTIONf_plane_restr0.00371024
X-RAY DIFFRACTIONf_dihedral_angle_d14.42132458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.690.61971110.51462425X-RAY DIFFRACTION88.8
2.69-2.740.48711490.50822555X-RAY DIFFRACTION93.79
2.74-2.780.46331440.47932633X-RAY DIFFRACTION96.46
2.78-2.830.47641250.45222571X-RAY DIFFRACTION93.9
2.83-2.880.47961540.42622669X-RAY DIFFRACTION96.88
2.88-2.940.41161380.40922646X-RAY DIFFRACTION99.18
2.94-30.43161400.39132793X-RAY DIFFRACTION99.36
3-3.060.45491430.37972680X-RAY DIFFRACTION99.26
3.06-3.130.35841520.38442742X-RAY DIFFRACTION99.35
3.13-3.210.42711310.35152702X-RAY DIFFRACTION99.09
3.21-3.30.38811530.32142709X-RAY DIFFRACTION99.17
3.3-3.390.38951440.31632691X-RAY DIFFRACTION99.3
3.39-3.50.30171420.28692745X-RAY DIFFRACTION99.21
3.5-3.630.3361410.26322721X-RAY DIFFRACTION99.34
3.63-3.770.32321350.24042718X-RAY DIFFRACTION99.03
3.77-3.940.22891530.22572702X-RAY DIFFRACTION98.75
3.95-4.150.20331310.18862594X-RAY DIFFRACTION94.06
4.15-4.410.22541430.19432695X-RAY DIFFRACTION98.27
4.41-4.750.23741320.1922712X-RAY DIFFRACTION99.65
4.75-5.230.23811540.19532722X-RAY DIFFRACTION99.79
5.23-5.980.23881420.25142720X-RAY DIFFRACTION99.65
5.99-7.540.2221470.23492720X-RAY DIFFRACTION98.9
7.54-47.870.22431350.1992638X-RAY DIFFRACTION96.35
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.77162132120.758398766267-0.5874386394422.26881750543-0.8948287584681.60648650987-0.166579265591-0.135319817772-0.119010546471-0.2852158515290.09034004504220.0590995099440.2231050795990.1240766588920.104366215890.6637006971270.112347541925-0.1828984828760.515556069234-0.08272628428420.70650091190970.868229555462.5269294764.26189452429
24.58587179676-0.1261992394161.144841167041.097998837550.5042389191962.19392980487-0.674515790921-0.6817505483510.711928854141-0.0003195422881820.1889235511120.119977606368-0.479128089019-0.1421635217360.4246372918861.10229034960.160402376804-0.4567587111130.87154502544-0.1089712416240.94441016098839.737053577368.227792089631.2475317187
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 30 through 438 )30 - 4381 - 409
22chain 'A' and (resid 439 through 771 )439 - 771410 - 742

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