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- PDB-9s96: Crystal structure of the BRL3 ectodomain from Arabidopsis thalian... -

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Basic information

Entry
Database: PDB / ID: 9s96
TitleCrystal structure of the BRL3 ectodomain from Arabidopsis thaliana in complex with typhasterol.
ComponentsReceptor-like protein kinase BRI1-like 3
KeywordsMEMBRANE PROTEIN / receptor kinase / steroid receptor / brassinosteroids / leucine-rich repeat
Function / homology
Function and homology information


steroid binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / ATP 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / 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
: / ACETATE ION / TRIETHYLENE GLYCOL / Receptor-like protein kinase BRI1-like 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.31 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 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Receptor-like protein kinase BRI1-like 3
B: Receptor-like protein kinase BRI1-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,77137
Polymers167,2392
Non-polymers13,53235
Water4,216234
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint116 kcal/mol
Surface area59670 Å2
Unit cell
Length a, b, c (Å)61.267, 81.848, 122.382
Angle α, β, γ (deg.)106.963, 91.770, 112.835
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Receptor-like protein kinase BRI1-like 3 / BRASSINOSTEROID INSENSITIVE 1-like protein 3


Mass: 83619.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BRL3, At3g13380, MRP15.1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9LJF3, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Sugars , 7 types, 22 molecules

#2: 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.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...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


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]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
DGlcpNAcb1-4[DManpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...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


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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.: 4 / 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 , 5 types, 247 molecules

#8: Chemical ChemComp-A1JMF / Typhasterol / (3~{R},5~{S},8~{S},9~{S},10~{R},13~{S},14~{R},17~{R})-17-[(2~{S},3~{R},4~{R},5~{S})-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.: 2 / Source method: obtained synthetically / Formula: C28H48O4
#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.19 Å3/Da / Density % sol: 61.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 23% PEG 3350, 0.2 M LiSO4, 0.1M sodium acetate pH 5.0, 25 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.31→47.24 Å / Num. obs: 83799 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 61.86 Å2 / CC1/2: 1 / Rrim(I) all: 0.071 / Net I/σ(I): 11
Reflection shellResolution: 2.31→2.45 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1 / Num. unique obs: 13781 / CC1/2: 0.586 / Rrim(I) all: 1.467 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.31→47.24 Å / SU ML: 0.3536 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.8126
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2365 4157 4.99 %
Rwork0.2091 79165 -
obs0.2105 83322 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.94 Å2
Refinement stepCycle: LAST / Resolution: 2.31→47.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10746 0 890 234 11870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003611836
X-RAY DIFFRACTIONf_angle_d0.668316092
X-RAY DIFFRACTIONf_chiral_restr0.05252072
X-RAY DIFFRACTIONf_plane_restr0.00391968
X-RAY DIFFRACTIONf_dihedral_angle_d13.56944839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.340.37781500.41742633X-RAY DIFFRACTION92.86
2.34-2.360.37541500.39382693X-RAY DIFFRACTION93.46
2.36-2.390.38681540.36642679X-RAY DIFFRACTION93.81
2.39-2.420.36681320.33652675X-RAY DIFFRACTION93.04
2.42-2.450.31541380.33572724X-RAY DIFFRACTION92.83
2.45-2.490.37941390.31832622X-RAY DIFFRACTION93.12
2.49-2.520.35241350.31242700X-RAY DIFFRACTION93.13
2.52-2.560.37881450.3062656X-RAY DIFFRACTION91.93
2.56-2.60.3021300.30112585X-RAY DIFFRACTION91.23
2.6-2.640.32921390.29532622X-RAY DIFFRACTION91.76
2.64-2.690.33761420.31282599X-RAY DIFFRACTION90.46
2.69-2.740.35071290.28842573X-RAY DIFFRACTION89.62
2.74-2.790.29211250.26832496X-RAY DIFFRACTION85.68
2.79-2.850.28591230.25872246X-RAY DIFFRACTION79.31
2.85-2.910.26311340.2572665X-RAY DIFFRACTION91.2
2.91-2.980.26781490.24632692X-RAY DIFFRACTION95.3
2.98-3.050.27031390.25262754X-RAY DIFFRACTION95.04
3.05-3.130.25911440.25492724X-RAY DIFFRACTION95.03
3.13-3.230.28071470.25882710X-RAY DIFFRACTION94.32
3.23-3.330.2931360.26292669X-RAY DIFFRACTION94.16
3.33-3.450.24621430.23952707X-RAY DIFFRACTION93.9
3.45-3.590.23481360.22582702X-RAY DIFFRACTION93.02
3.59-3.750.23161390.19792606X-RAY DIFFRACTION91.78
3.75-3.950.24071320.19562577X-RAY DIFFRACTION89.35
3.95-4.20.19341250.16722300X-RAY DIFFRACTION80.38
4.2-4.520.17081410.1552775X-RAY DIFFRACTION95.83
4.52-4.970.19391410.14982752X-RAY DIFFRACTION96.43
4.98-5.690.2011450.17372751X-RAY DIFFRACTION95.45
5.69-7.170.22961370.19482657X-RAY DIFFRACTION92.64
7.17-47.240.19941380.16482621X-RAY DIFFRACTION90.97
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)
11.29399556684-0.300443296747-0.2812313944920.9473388943070.3554823033361.582260672690.0727488386760.0920424460088-0.2422592168-0.0326542779229-0.0971421214765-0.02202817696810.168722610831-0.0917541880207-0.03063668333940.6188305782980.0285013707095-0.05990700531330.6105174040840.01852159097960.514433518969-19.32904959414.261025968577.6019688618
22.59105510165-0.740199476557-1.732688170691.839511448772.00969903256.604631227680.09626331017-0.05379489718080.037361031232-0.0386429142696-0.00904526226076-0.00831030900345-0.182147330807-0.104319132948-0.123232016260.5631405695150.0692624437515-0.01047955598190.5058747705130.08556737221610.459018086748-25.794348353435.833358601595.1106225963
31.078888288370.1136193176781.07727801171.820639523480.8457652544483.940618275130.0676901494844-0.04948740662550.181397910683-0.163007158628-0.169937290841-0.0709457617877-0.508431143529-0.03094645155640.08415310907360.7411977601610.01843499745350.08382615209820.7150222859050.09339237727190.618201292928-23.506078480942.6060556792114.859637114
41.28265641921.21073890573-0.8839295034633.11036222087-1.074344754831.79338224765-0.2853763199560.216438485573-0.264898721313-0.5202739854710.128365359358-0.5973540170950.088474563140.07143383282770.1744879294530.709227113875-0.0895097758480.1108241299510.641313723314-0.06413905289140.77914841671628.063517323441.463239419520.1631014811
50.878081148882-0.598060294652-0.09937056809992.60309367127-0.2572589489851.11850968188-0.155323212812-0.153601234941-0.04157993386410.6223583022190.0979322825824-0.105635270109-0.1176947221670.02735033470360.0326702105740.6398507619570.0044210046321-0.07461689687080.53602772844-0.01935109884710.4778244257724.8291602466347.749374805951.7711554092
61.94094943623-1.298274084341.179806367634.29667793616-1.873840858652.71498209169-0.0871556598119-0.0674093568510.07257622929860.1786663993130.194368698271-0.0241993193402-0.234844813078-0.0842506666067-0.02875526312870.5425128895310.01734668201690.05300044560530.488941200219-0.032038777660.449942090163-7.294992571868.716608073636.6412103174
72.1739792682-0.522498133711.921073007072.75702282177-0.8109531382743.56241362482-0.1293562296640.1446984240830.0196548560037-0.06054290579490.1300734908070.118787662198-0.0949549554909-0.29702308446-0.1252309939460.617178657581-0.03554472282170.06129757876220.59849451220.02584916326090.542968070588-19.621118514375.768186701620.6979360146
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 32 through 553 )AA32 - 5531 - 515
22chain 'A' and (resid 554 through 669 )AA554 - 669516 - 627
33chain 'A' and (resid 670 through 757 )AA670 - 757628 - 715
44chain 'B' and (resid 32 through 219 )BB32 - 2191 - 184
55chain 'B' and (resid 220 through 529 )BB220 - 529185 - 494
66chain 'B' and (resid 530 through 669 )BB530 - 669495 - 631
77chain 'B' and (resid 670 through 758 )BB670 - 758632 - 720

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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