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- PDB-3riz: Crystal structure of the plant steroid receptor BRI1 ectodomain -

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Entry
Database: PDB / ID: 3riz
TitleCrystal structure of the plant steroid receptor BRI1 ectodomain
ComponentsProtein BRASSINOSTEROID INSENSITIVE 1
KeywordsSIGNALING PROTEIN / superhelix / 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 / 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 / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / 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
Protein BRASSINOSTEROID INSENSITIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.523 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.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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
Revision 2.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)86,0807
Polymers83,4941
Non-polymers2,5856
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.093, 67.251, 119.050
Angle α, β, γ (deg.)90.00, 121.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-863-

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.: 2
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: 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.: 1
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
#4: 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.: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.59 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: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9998
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.52→31 Å / Num. all: 40152 / Num. obs: 39686 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.055 / Net I/σ(I): 17.6
Reflection shellResolution: 2.52→2.68 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.583 / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.523→30.989 Å / SU ML: 0.4 / σ(F): 1.32 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1980 4.99 %
Rwork0.1871 --
obs0.1897 39686 99.18 %
all-39686 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.195 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.9382 Å20 Å2-0.1178 Å2
2--1.1013 Å2-0 Å2
3----0.5909 Å2
Refinement stepCycle: LAST / Resolution: 2.523→30.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5543 0 170 129 5842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065899
X-RAY DIFFRACTIONf_angle_d1.0188024
X-RAY DIFFRACTIONf_dihedral_angle_d18.6492206
X-RAY DIFFRACTIONf_chiral_restr0.067963
X-RAY DIFFRACTIONf_plane_restr0.0041018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.523-2.58610.48371260.38722417X-RAY DIFFRACTION90
2.5861-2.65590.41481400.32432674X-RAY DIFFRACTION100
2.6559-2.7340.33181420.25742704X-RAY DIFFRACTION100
2.734-2.82220.29251420.22442706X-RAY DIFFRACTION100
2.8222-2.9230.30911410.22162704X-RAY DIFFRACTION100
2.923-3.040.28081410.22552698X-RAY DIFFRACTION100
3.04-3.17820.30321420.2162685X-RAY DIFFRACTION100
3.1782-3.34560.26751430.21882725X-RAY DIFFRACTION100
3.3456-3.55490.28811420.20082694X-RAY DIFFRACTION100
3.5549-3.82890.20841420.1652706X-RAY DIFFRACTION100
3.8289-4.21340.17441430.13252731X-RAY DIFFRACTION100
4.2134-4.82110.16731440.12642723X-RAY DIFFRACTION100
4.8211-6.06660.22761430.16962740X-RAY DIFFRACTION100
6.0666-30.99140.22021490.19852799X-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)
11.64791.04190.06261.5926-0.69780.5654-0.09880.26510.3978-0.28010.16780.3439-0.1753-0.0252-0.00320.2205-0.0115-0.00040.09950.02250.288372.330379.4325-9.1213
21.48190.0157-1.03960.85930.35161.7261-0.5677-0.3526-0.6044-0.18420.25090.05790.65730.44530.0520.18450.25030.11630.26330.09740.410171.643448.178713.2162
31.63060.0574-0.0620.54810.3680.8752-0.4188-1.01330.39770.40930.32920.0227-0.2460.46170.04020.18210.0761-0.20340.5831-0.10870.196953.498167.890537.1394
42.85710.04720.75492.0574-0.23510.3973-0.3984-0.35690.0838-0.12350.1514-0.4926-0.06550.0510.1870.42410.1313-0.04320.40980.0190.368438.925367.280827.1818
51.7038-0.80980.47970.9548-0.2940.1572-0.0487-0.33650.2927-0.19450.00910.134-0.3392-0.27680.08490.40830.1878-0.13260.4294-0.0330.280819.339171.155523.1431
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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