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- PDB-9s80: Crystal structure of the BRL3 ectodomain from Arabidopsis thalian... -

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Basic information

Entry
Database: PDB / ID: 9s80
TitleCrystal structure of the BRL3 ectodomain from Arabidopsis thaliana in complex with brassinolide.
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 / Brassinolide / GLYCINE / Receptor-like protein kinase BRI1-like 3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHohmann, U. / 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

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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)179,86637
Polymers165,2232
Non-polymers14,64335
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19510 Å2
ΔGint200 kcal/mol
Surface area60390 Å2
Unit cell
Length a, b, c (Å)60.457, 81.762, 122.190
Angle α, β, γ (deg.)107.238, 91.941, 112.386
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: 82611.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0 / Gene: BRL3, At3g13380, MRP15.1 / Plasmid: pBB2 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tnao38
References: UniProt: Q9LJF3, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Sugars , 5 types, 25 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.: 2
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 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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
#7: 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.: 7 / 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 , 7 types, 200 molecules

#6: Chemical ChemComp-BLD / Brassinolide / (3aS,5S,6R,7aR,7bS,9aS,10R,12aS,12bS)-10-[(2S,3R,4R,5S)-3,4-dihydroxy-5,6-dimethylheptan-2-yl]-5,6-dihydroxy-7a,9a-dime thylhexadecahydro-3H-benzo[c]indeno[5,4-e]oxepin-3-one


Mass: 480.677 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H48O6
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#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.: 190 / 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: 3.18 Å3/Da / Density % sol: 61.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 23% PEG 3350, 0.2 M LiSo4, 01. citric acid pH 4.0, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 2.45→48.66 Å / Num. obs: 73350 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 50.87 Å2 / CC1/2: 1 / Rrim(I) all: 0.122 / Net I/σ(I): 9.85
Reflection shellResolution: 2.45→2.6 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 11727 / CC1/2: 0.52 / Rrim(I) all: 1.392 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→48.66 Å / SU ML: 0.3988 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.6207
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2579 3666 5 %
Rwork0.2216 69631 -
obs0.2234 73297 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.59 Å2
Refinement stepCycle: LAST / Resolution: 2.45→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10832 0 970 190 11992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003712048
X-RAY DIFFRACTIONf_angle_d0.739816383
X-RAY DIFFRACTIONf_chiral_restr0.0412126
X-RAY DIFFRACTIONf_plane_restr0.00562005
X-RAY DIFFRACTIONf_dihedral_angle_d15.99435198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.37961350.36642557X-RAY DIFFRACTION94.13
2.48-2.520.39431430.38222701X-RAY DIFFRACTION97.4
2.52-2.550.39131400.3592654X-RAY DIFFRACTION97.52
2.55-2.590.38171390.35782639X-RAY DIFFRACTION97.68
2.59-2.630.37191430.34922723X-RAY DIFFRACTION98.02
2.63-2.680.34641380.32732629X-RAY DIFFRACTION98.02
2.68-2.720.36031440.31672731X-RAY DIFFRACTION97.96
2.72-2.770.30141390.2852640X-RAY DIFFRACTION98.23
2.77-2.820.32861420.28372702X-RAY DIFFRACTION98.17
2.82-2.880.28561420.28912681X-RAY DIFFRACTION97.99
2.88-2.940.31091390.27622659X-RAY DIFFRACTION98.11
2.94-3.010.3441450.28832752X-RAY DIFFRACTION98.37
3.01-3.090.3021380.29112622X-RAY DIFFRACTION97.98
3.09-3.170.37281420.29492695X-RAY DIFFRACTION98.3
3.17-3.260.30341410.26732697X-RAY DIFFRACTION98.27
3.26-3.370.30841430.26522715X-RAY DIFFRACTION98.59
3.37-3.490.24211400.24882658X-RAY DIFFRACTION98.49
3.49-3.630.26291420.22242700X-RAY DIFFRACTION98.65
3.63-3.80.27581420.21192684X-RAY DIFFRACTION97.85
3.8-40.21821410.18292675X-RAY DIFFRACTION98.08
4-4.250.22691420.16762701X-RAY DIFFRACTION98.78
4.25-4.570.19011420.16252695X-RAY DIFFRACTION98.34
4.57-5.030.20941410.16162690X-RAY DIFFRACTION98.47
5.03-5.760.23621410.18542676X-RAY DIFFRACTION98.32
5.76-7.250.2141420.18842687X-RAY DIFFRACTION97.82
7.25-48.660.19411400.16612668X-RAY DIFFRACTION97.84

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