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- PDB-4lsa: Crystal structure of BRI1 sud1 (Gly643Glu) bound to brassinolide -

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Basic information

Entry
Database: PDB / ID: 4lsa
TitleCrystal structure of BRI1 sud1 (Gly643Glu) bound to brassinolide
ComponentsProtein BRASSINOSTEROID INSENSITIVE 1
KeywordsSTEROID BINDING PROTEIN / LRR-domain / membrane receptor / brassinosteroid binding / N-glycosylation / protein binding
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 / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / GPI-linked ephrin receptor activity / transmembrane-ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / endosome / endosome membrane / 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
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSantiago, J. / Henzler, C. / Hothorn, M.
CitationJournal: Science / Year: 2013
Title: Molecular mechanism for plant steroid receptor activation by somatic embryogenesis co-receptor kinases.
Authors: Santiago, J. / Henzler, C. / Hothorn, M.
History
DepositionJul 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
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 / 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 / _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_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein BRASSINOSTEROID INSENSITIVE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3389
Polymers83,7271
Non-polymers3,6128
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.033, 67.303, 120.901
Angle α, β, γ (deg.)90.00, 121.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 83726.594 Da / Num. of mol.: 1
Fragment: receptor ectodomain/LRR-domain (UNP residues 29-788)
Mutation: G643E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: col 0 / Gene: At4g39400, BRI1, F23K16.30 / Plasmid: pBAC-6 mod. / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Tnao38 / References: UniProt: O22476
#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-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: 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


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


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
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: 3.62 Å3/Da / Density % sol: 66.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 23% 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: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97963 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97963 Å / Relative weight: 1
ReflectionResolution: 2.5→49.56 Å / Num. all: 41658 / Num. obs: 41658 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.75 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.05 / Net I/σ(I): 20.74
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.08 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 1.81 / Num. unique all: 2889 / Rsym value: 0.955 / % possible all: 88.5

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1334)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RJ0

3rj0


Resolution: 2.5→49.557 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 30.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 2084 5.03 %RANDOM
Rwork0.2053 ---
obs0.2075 41532 99.32 %-
all-41658 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→49.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5541 0 240 49 5830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035948
X-RAY DIFFRACTIONf_angle_d0.7428113
X-RAY DIFFRACTIONf_dihedral_angle_d18.3322188
X-RAY DIFFRACTIONf_chiral_restr0.042993
X-RAY DIFFRACTIONf_plane_restr0.0021020
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52890.45011290.38852310X-RAY DIFFRACTION86
2.5289-2.55970.40971500.3652632X-RAY DIFFRACTION100
2.5597-2.59210.40741410.35912677X-RAY DIFFRACTION100
2.5921-2.62630.46641370.32632589X-RAY DIFFRACTION100
2.6263-2.66220.39921420.30852748X-RAY DIFFRACTION99
2.6622-2.70030.28761560.29332578X-RAY DIFFRACTION100
2.7003-2.74060.35781340.28582633X-RAY DIFFRACTION100
2.7406-2.78340.33951410.28152679X-RAY DIFFRACTION100
2.7834-2.8290.30811550.28552682X-RAY DIFFRACTION100
2.829-2.87780.32861270.28332648X-RAY DIFFRACTION100
2.8778-2.93010.3931250.27442710X-RAY DIFFRACTION100
2.9301-2.98650.32091390.27632569X-RAY DIFFRACTION100
2.9865-3.04740.2361500.26412683X-RAY DIFFRACTION100
3.0474-3.11370.39191420.27512679X-RAY DIFFRACTION100
3.1137-3.18610.28171420.24362671X-RAY DIFFRACTION100
3.1861-3.26570.31721230.23012652X-RAY DIFFRACTION100
3.2657-3.3540.29581550.24632677X-RAY DIFFRACTION100
3.354-3.45270.24231430.22482640X-RAY DIFFRACTION100
3.4527-3.56410.28621320.22172695X-RAY DIFFRACTION100
3.5641-3.69150.28651420.19032662X-RAY DIFFRACTION100
3.6915-3.83920.24381270.17722637X-RAY DIFFRACTION100
3.8392-4.01390.21151510.16252659X-RAY DIFFRACTION100
4.0139-4.22540.19661390.14652669X-RAY DIFFRACTION100
4.2254-4.48990.19181440.14142680X-RAY DIFFRACTION100
4.4899-4.83630.20161340.14992662X-RAY DIFFRACTION100
4.8363-5.32250.20061430.15452641X-RAY DIFFRACTION100
5.3225-6.09150.18941400.18872673X-RAY DIFFRACTION100
6.0915-7.67010.20041460.20262633X-RAY DIFFRACTION100
7.6701-49.56650.22811370.20432661X-RAY DIFFRACTION99
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)
12.19051.30880.35016.5395-0.3231.4625-0.13410.31770.2015-0.42560.15140.3265-0.1994-0.133-0.02440.42840.0104-0.05420.33250.00190.508371.393877.2783-8.5463
23.4545-0.752-2.23841.09280.23654.7187-0.4519-1.0223-0.72510.26760.22130.05270.71190.75840.17950.52530.1370.01050.56820.14320.730571.608746.460213.8219
34.7128-0.79620.70141.58830.36283.1891-0.6791-1.64080.80770.3430.3941-0.3972-0.38180.37050.2790.67710.1623-0.18331.2204-0.17850.623754.214367.192937.1029
49.2728-2.95710.034.0290.08842.3466-0.7009-1.16440.38850.0770.46850.1451-0.0614-0.11370.23050.6040.0982-0.16110.6711-0.06430.399139.880765.462526.9741
54.46762.4553-1.14625.2253-0.75520.9777-0.4777-0.77340.8072-0.12460.17080.6023-0.42-0.3920.30870.6320.2078-0.17860.7436-0.09560.574619.836369.552622.8087
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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