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- PDB-3rj0: Plant steroid receptor BRI1 ectodomain in complex with brassinolide -

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Basic information

Entry
Database: PDB / ID: 3rj0
TitlePlant steroid receptor BRI1 ectodomain in complex with brassinolide
ComponentsProtein BRASSINOSTEROID INSENSITIVE 1
KeywordsSIGNALING PROTEIN / superhelix / island domain / Leucine-rich repeat / steroid receptor / hormone receptor / receptor kinase / brassinosteroid binding / N-glycosylation / plasma membrane and endosomes
Function / homology
Function and homology information


detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / microtubule bundle formation ...detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / seedling development / skotomorphogenesis / positive regulation of flower development / brassinosteroid mediated signaling pathway / leaf development / microtubule bundle formation / response to UV-B / steroid binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / endosome membrane / non-specific serine/threonine protein kinase / endosome / protein kinase activity / protein heterodimerization activity / phosphorylation / 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
Dna Ligase; domain 1 - #310 / 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, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat ...Dna Ligase; domain 1 - #310 / 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, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Dna Ligase; domain 1 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Brassinolide / Protein BRASSINOSTEROID INSENSITIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.541 Å
AuthorsHothorn, M.
CitationJournal: Nature / Year: 2011
Title: Structural basis of steroid hormone perception by the receptor kinase BRI1.
Authors: Hothorn, M. / Belkhadir, Y. / Dreux, M. / Dabi, T. / Noel, J.P. / Wilson, I.A. / Chory, J.
History
DepositionApr 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)86,8858
Polymers83,4941
Non-polymers3,3907
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.170, 67.236, 119.246
Angle α, β, γ (deg.)90.00, 121.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-876-

HOH

21A-888-

HOH

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Components

#1: Protein Protein BRASSINOSTEROID INSENSITIVE 1 / BRI1 / Brassinosteroid LRR receptor kinase / AtBRI1


Mass: 83494.398 Da / Num. of mol.: 1 / Fragment: ectodomain (UNP residues 29-788)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g39400, BRI1, F23K16.30 / Plasmid: pBAC-6 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5
References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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
#4: 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 / Brassinolide


Mass: 480.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H48O6 / Comment: hormone*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O

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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: 3.59 Å3/Da / Density % sol: 65.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 14% PEG4000, 0.2 M ammonium sulfate, 0.1 M citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 22, 2010 / Details: osmic mirrors
RadiationMonochromator: copper Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.54→24.64 Å / Num. all: 39452 / Num. obs: 38900 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 51.8 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.9
Reflection shellResolution: 2.54→2.63 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 5904 / Rsym value: 0.482 / % possible all: 93.8

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Processing

Software
NameVersionClassification
StructureStudiodata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.541→24.637 Å / SU ML: 0.36 / σ(F): 2 / Phase error: 25.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1943 5 %RANDOM
Rwork0.1839 ---
obs0.1867 38849 98.85 %-
all-39300 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.746 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 51.8 Å2
Baniso -1Baniso -2Baniso -3
1--6.1532 Å2-0 Å2-4.786 Å2
2--3.0658 Å20 Å2
3---3.0874 Å2
Refinement stepCycle: LAST / Resolution: 2.541→24.637 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5557 0 226 114 5897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065974
X-RAY DIFFRACTIONf_angle_d1.0538141
X-RAY DIFFRACTIONf_dihedral_angle_d21.2292279
X-RAY DIFFRACTIONf_chiral_restr0.067990
X-RAY DIFFRACTIONf_plane_restr0.0041023
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5411-2.60450.36061290.2822335X-RAY DIFFRACTION88
2.6045-2.67490.33041400.25782623X-RAY DIFFRACTION99
2.6749-2.75350.27051380.23392634X-RAY DIFFRACTION100
2.7535-2.84220.29151370.22652644X-RAY DIFFRACTION100
2.8422-2.94370.33031370.2322626X-RAY DIFFRACTION100
2.9437-3.06130.32221420.23832659X-RAY DIFFRACTION100
3.0613-3.20040.29171380.22872639X-RAY DIFFRACTION100
3.2004-3.36870.27751390.21362653X-RAY DIFFRACTION100
3.3687-3.57920.25441410.19822639X-RAY DIFFRACTION100
3.5792-3.85460.24881380.16022659X-RAY DIFFRACTION100
3.8546-4.24070.16641410.14252683X-RAY DIFFRACTION100
4.2407-4.85020.19311390.12792668X-RAY DIFFRACTION100
4.8502-6.09550.22091420.17032693X-RAY DIFFRACTION100
6.0955-24.6380.22331420.18752751X-RAY DIFFRACTION100
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)
12.01550.82910.2632.2058-0.39920.9031-0.05270.20050.3685-0.21730.13940.3139-0.1595-0.0713-0.06930.1685-0.01540.02460.06370.0210.230272.215679.4859-9.0839
23.3254-0.4763-2.12450.64551.1232.1667-0.5595-0.5236-0.77650.00310.22780.12080.56280.51730.33160.24950.17010.10570.21710.1280.451971.696948.131313.2125
34.4158-0.5302-0.49810.90030.16881.679-0.6893-1.76330.72090.430.45-0.3323-0.05880.28760.12190.26240.2381-0.18830.7495-0.26120.249653.69167.828837.2174
45.0963-1.58080.18521.58660.27560.3621-0.6424-1.01220.37410.20850.4735-0.1763-0.0752-0.03430.13980.40580.1839-0.06530.4554-0.04010.219939.299167.198827.0471
52.7553-1.26870.88661.553-0.42780.2843-0.4271-0.70150.4855-0.05030.290.1024-0.1965-0.43990.14410.39730.198-0.10240.4673-0.05050.277219.525171.274823.0892
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 29:221)
2X-RAY DIFFRACTION2(chain A and resid 222:416)
3X-RAY DIFFRACTION3(chain A and resid 417:587)
4X-RAY DIFFRACTION4(chain A and resid 588:702)
5X-RAY DIFFRACTION5(chain A and resid 703:771)

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