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- PDB-4oh4: Crystal structure of BRI1 in complex with BKI1 -

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Basic information

Entry
Database: PDB / ID: 4oh4
TitleCrystal structure of BRI1 in complex with BKI1
Components
  • BRI1 kinase inhibitor 1
  • Protein BRASSINOSTEROID INSENSITIVE 1
KeywordsTRANSFERASE/SIGNALING PROTEIN / kinase domain / transferase / ATP binding / Phosphorylation / Membrane / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


negative regulation of brassinosteroid biosynthetic process / 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 ...negative regulation of brassinosteroid biosynthetic process / 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 / protein kinase inhibitor activity / steroid binding / transmembrane receptor protein tyrosine kinase activity / lipid metabolic process / 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 / cytosol
Similarity search - Function
BKI1/Probable membrane-associated kinase regulator 1/3/4 / 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, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat ...BKI1/Probable membrane-associated kinase regulator 1/3/4 / 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, 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Protein BRASSINOSTEROID INSENSITIVE 1 / BRI1 kinase inhibitor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWang, J. / Wang, J. / Wu, J.W. / Wang, Z.X.
CitationJournal: Cell Res. / Year: 2014
Title: Structural insights into the negative regulation of BRI1 signaling by BRI1-interacting protein BKI1.
Authors: Wang, J. / Jiang, J. / Wang, J. / Chen, L. / Fan, S.L. / Wu, J.W. / Wang, X. / Wang, Z.X.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein BRASSINOSTEROID INSENSITIVE 1
B: Protein BRASSINOSTEROID INSENSITIVE 1
F: BRI1 kinase inhibitor 1
E: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6876
Polymers79,6744
Non-polymers1,0122
Water3,801211
1
A: Protein BRASSINOSTEROID INSENSITIVE 1
E: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3433
Polymers39,8372
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-17 kcal/mol
Surface area15610 Å2
MethodPISA
2
B: Protein BRASSINOSTEROID INSENSITIVE 1
F: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3433
Polymers39,8372
Non-polymers5061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-16 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.915, 80.139, 79.623
Angle α, β, γ (deg.)90.00, 108.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 37555.660 Da / Num. of mol.: 2 / Fragment: kinase domain, UNP residues 863-1172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g39400, BRI1, F23K16.30 / Plasmid: pET-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O22476, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide BRI1 kinase inhibitor 1


Mass: 2281.564 Da / Num. of mol.: 2 / Fragment: C-terminal peptide, UNP residues 306-325 / Source method: obtained synthetically
Details: This sequence occurs naturally in Arabidopsis thaliana.
Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q9FMZ0
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M Lithium Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 35679 / Num. obs: 35446 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Biso Wilson estimate: 45.77 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 25.4
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3525 / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QKW

2qkw


Resolution: 2.25→37.839 Å / SU ML: 0.32 / σ(F): 1.34 / Phase error: 32.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 1770 4.99 %RANDOM
Rwork0.2016 ---
obs0.2034 35446 99.38 %-
all-35679 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.228 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-58.9486 Å2-0 Å2-16.5973 Å2
2--18.815 Å20 Å2
3---3.0378 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4967 0 62 211 5240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095130
X-RAY DIFFRACTIONf_angle_d1.3376944
X-RAY DIFFRACTIONf_dihedral_angle_d18.391904
X-RAY DIFFRACTIONf_chiral_restr0.098768
X-RAY DIFFRACTIONf_plane_restr0.005869
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.31080.35551270.35292556X-RAY DIFFRACTION98
2.3108-2.37880.38151230.29862571X-RAY DIFFRACTION99
2.3788-2.45560.35851350.26112597X-RAY DIFFRACTION100
2.4556-2.54330.27461410.23452586X-RAY DIFFRACTION100
2.5433-2.64510.30351280.23662604X-RAY DIFFRACTION100
2.6451-2.76550.24461350.22742596X-RAY DIFFRACTION100
2.7655-2.91120.26641300.232601X-RAY DIFFRACTION100
2.9112-3.09360.26221430.2312573X-RAY DIFFRACTION100
3.0936-3.33230.24981330.21792615X-RAY DIFFRACTION100
3.3323-3.66740.2571350.19042600X-RAY DIFFRACTION100
3.6674-4.19750.21331470.16352619X-RAY DIFFRACTION100
4.1975-5.28610.16961420.16042597X-RAY DIFFRACTION100
5.2861-37.8440.22341510.19822561X-RAY DIFFRACTION96
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)
11.70821.24850.53043.71192.18163.3635-0.1364-0.23250.4070.5262-0.1144-0.1178-0.46680.03020.15320.3873-0.0343-0.1350.1796-0.03420.3679-14.699816.0523104.1711
22.17820.98161.71423.07540.84324.40740.2352-0.7109-0.01940.8537-0.240.1960.6888-0.9871-0.00530.3073-0.2220.09690.33090.04150.1379-25.0175-2.2943106.3828
31.41850.62150.93510.82710.56533.85150.10830.02930.481.0363-0.2308-0.5215-0.8810.52610.12130.7793-0.2992-0.42030.3381-0.080.4871-15.575444.662784.3833
42.01470.8376-0.5712.41061.34844.2639-0.1617-0.0209-0.15851.17450.1505-0.67410.09040.9687-0.01460.6750.0109-0.29020.555-0.05950.4832-12.865237.501389.0346
52.7473-0.26161.01432.9412-1.23174.5876-0.0189-0.18730.08460.61810.085-0.2441-0.07370.2265-0.0750.2310.0642-0.04120.1671-0.02340.1725-23.638733.348879.3502
63.9458-0.4042-1.01581.23650.9623.8870.4195-0.8399-0.63541.291-0.26070.51511.5174-1.5018-0.04420.4423-0.23130.29780.82710.25330.3317-42.74126.417184.6178
73.78720.00370.26572.7126-0.20485.6350.1841-0.1095-0.12430.32460.20490.60070.6951-1.1811-0.0826-0.01650.01220.07620.39240.07570.28-38.523229.082770.036
80.40340.12311.34342.02480.07614.5414-0.2690.3422-0.7972-0.10780.08290.30390.4428-0.02470.11340.5146-0.88280.20761.6050.24810.9966-51.22521.556176.036
91.50231.3353-0.94335.0406-0.57014.5473-0.10610.3809-0.3768-0.04430.0366-0.25010.47720.04450.15161.8079-1.43090.35690.40240.52560.5016-37.1324-20.4441108.5528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 852:933 )A852 - 933
2X-RAY DIFFRACTION2( CHAIN A AND RESID 934:1160 )A934 - 1160
3X-RAY DIFFRACTION3( CHAIN B AND RESID 852:887 )B852 - 887
4X-RAY DIFFRACTION4( CHAIN B AND RESID 888:928 )B888 - 928
5X-RAY DIFFRACTION5( CHAIN B AND RESID 929:1064 )B929 - 1064
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1065:1137 )B1065 - 1137
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1138:1160 )B1138 - 1160
8X-RAY DIFFRACTION8( CHAIN F AND RESID 307:322 )F307 - 322
9X-RAY DIFFRACTION9( CHAIN E AND RESID 307:322 )E307 - 322

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