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- PDB-6fif: Crystal structure of the BRI1 Gly644-Asp (bri1-6) mutant from Ara... -

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Basic information

Entry
Database: PDB / ID: 6fif
TitleCrystal structure of the BRI1 Gly644-Asp (bri1-6) mutant from Arabidopsis thaliana.
ComponentsProtein BRASSINOSTEROID INSENSITIVE 1
KeywordsPROTEIN BINDING / leucine rich repeat receptor / membrane receptor / ectodomain
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
Protein BRASSINOSTEROID INSENSITIVE 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsHothorn, M. / Santiago, J. / Hohmann, U.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_156920 Switzerland
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanistic basis for the activation of plant membrane receptor kinases by SERK-family coreceptors.
Authors: Hohmann, U. / Santiago, J. / Nicolet, J. / Olsson, V. / Spiga, F.M. / Hothorn, L.A. / Butenko, M.A. / Hothorn, M.
History
DepositionJan 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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_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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)93,81010
Polymers90,8571
Non-polymers2,9539
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, gel filtration, isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint46 kcal/mol
Surface area31080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.684, 67.569, 151.850
Angle α, β, γ (deg.)90.00, 100.65, 90.00
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 90857.438 Da / Num. of mol.: 1 / Mutation: Gly644-Asp
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BRI1, At4g39400, F23K16.30 / Organ: seedling / Cell line (production host): Tnao-37 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase

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Sugars , 4 types, 8 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.: 2
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 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
#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.: 1
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: 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 / N-Acetylglucosamine


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

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Non-polymers , 2 types, 28 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.32 Å3/Da / Density % sol: 62.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 18% [w/v] PEG 4,000, 0.2 M (NH4)2SO4, 0.1 M citric acid pH 4.0

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97963 Å / Relative weight: 1
ReflectionResolution: 2.54→19.89 Å / Num. obs: 39088 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 65.6 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.071 / Rsym value: 0.064 / Net I/σ(I): 13.9
Reflection shellResolution: 2.54→2.69 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5972 / CC1/2: 0.78 / Rrim(I) all: 1.25 / Rsym value: 1.12 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RIZ

3riz


Resolution: 2.54→19.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 30.327 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.262 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25447 1898 4.9 %RANDOM
Rwork0.20477 ---
obs0.2071 37172 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 87.966 Å2
Baniso -1Baniso -2Baniso -3
1-5.21 Å20 Å21.17 Å2
2---0.77 Å2-0 Å2
3----4.56 Å2
Refinement stepCycle: 1 / Resolution: 2.54→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 193 27 5792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195958
X-RAY DIFFRACTIONr_bond_other_d0.0020.025404
X-RAY DIFFRACTIONr_angle_refined_deg1.9282.0268132
X-RAY DIFFRACTIONr_angle_other_deg1.089312668
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3465759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11225.683227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.08315964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8931517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216539
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021074
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1364.4732994
X-RAY DIFFRACTIONr_mcbond_other3.1334.4732993
X-RAY DIFFRACTIONr_mcangle_it4.9066.7143746
X-RAY DIFFRACTIONr_mcangle_other4.9066.7143747
X-RAY DIFFRACTIONr_scbond_it4.6915.2012964
X-RAY DIFFRACTIONr_scbond_other4.6895.2012964
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4797.7034380
X-RAY DIFFRACTIONr_long_range_B_refined11.11589.3924288
X-RAY DIFFRACTIONr_long_range_B_other11.11589.39124289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.542→2.606 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 112 -
Rwork0.386 2449 -
obs--89.11 %
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)
10.50561.49990.37267.15671.48911.2068-0.11990.2540.0416-0.66610.2375-0.2977-0.33280.2719-0.11770.3497-0.0057-0.06020.41230.00880.1603-0.389546.7038-17.7747
26.71980.3391-0.50051.8844-0.67491.5677-0.0228-0.9507-0.92180.10380.24690.26370.3041-0.2883-0.22410.3002-0.0099-0.15160.46810.15540.2852-19.376515.3825-6.3406
34.225-1.6221.88312.0958-0.6624.3849-0.1931-0.97150.13670.30460.2955-0.2175-1.088-0.5602-0.10230.48190.15270.03260.91210.03010.0345-49.35735.0823-9.5872
411.5434-5.4591.81278.7708-6.25064.99350.24870.2141-0.5086-0.3129-0.04470.29580.2407-0.0318-0.2040.72860.1095-0.0880.88620.10750.3568-46.418824.34-22.3122
55.08450.8030.92993.63420.09828.129-0.0201-0.25380.00780.08830.1242-0.2742-0.6846-0.2172-0.10420.47450.10550.07690.47610.08310.0509-52.482139.9609-38.7905
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 221
2X-RAY DIFFRACTION2A222 - 416
3X-RAY DIFFRACTION3A417 - 588
4X-RAY DIFFRACTION4A589 - 635
5X-RAY DIFFRACTION5A636 - 772

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