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- PDB-4q5j: Crystal structure of SeMet derivative BRI1 in complex with BKI1 -

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Basic information

Entry
Database: PDB / ID: 4q5j
TitleCrystal structure of SeMet derivative BRI1 in complex with BKI1
Components
  • BRI1 kinase inhibitor 1
  • Protein BRASSINOSTEROID INSENSITIVE 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase domain / ATP binding / Phosphorylation / SeMet labelled / Membrane / TRANSFERASE-TRANSFERASE INHIBITOR 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 / positive regulation of flower development / seedling development / brassinosteroid mediated signaling pathway / leaf development / response to UV-B ...negative regulation of brassinosteroid biosynthetic process / detection of brassinosteroid stimulus / brassinosteroid homeostasis / anther wall tapetum cell differentiation / pollen exine formation / positive regulation of flower development / seedling development / brassinosteroid mediated signaling pathway / leaf development / response to UV-B / protein kinase inhibitor activity / steroid binding / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / lipid metabolic process / protein kinase activity / non-specific serine/threonine protein kinase / 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 / 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: 2.772 Å
AuthorsWang, J. / Wang, J. / Chen, L. / 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
DepositionApr 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.2Nov 8, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)83,5206
Polymers82,5074
Non-polymers1,0122
Water362
1
A: Protein BRASSINOSTEROID INSENSITIVE 1
E: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7603
Polymers41,2542
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-15 kcal/mol
Surface area15330 Å2
MethodPISA
2
B: Protein BRASSINOSTEROID INSENSITIVE 1
F: BRI1 kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7603
Polymers41,2542
Non-polymers5061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-18 kcal/mol
Surface area15160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.715, 80.288, 80.557
Angle α, β, γ (deg.)90.00, 109.55, 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: 38972.102 Da / Num. of mol.: 2 / Fragment: kinase domain, UNP residues 863-1180
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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 0.2M ithium 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: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. all: 19482 / Num. obs: 19437 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Biso Wilson estimate: 71.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 22.6
Reflection shellResolution: 2.77→2.87 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 4.1 / Num. unique all: 1906 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OH4

4oh4


Resolution: 2.772→38.409 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 36.04 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 994 5.11 %RANDOM
Rwork0.2005 ---
obs0.2035 19437 99.37 %-
all-19482 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.772→38.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4848 0 62 2 4912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135008
X-RAY DIFFRACTIONf_angle_d1.5186792
X-RAY DIFFRACTIONf_dihedral_angle_d18.9891820
X-RAY DIFFRACTIONf_chiral_restr0.057765
X-RAY DIFFRACTIONf_plane_restr0.007847
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.772-2.91830.34611390.2752256297
2.9183-3.10110.31011390.24172621100
3.1011-3.34040.27971440.23352629100
3.3404-3.67630.28011530.21082635100
3.6763-4.20770.22671290.16592655100
4.2077-5.29910.19131660.16992626100
5.2991-38.41310.29811240.2114271599
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)
11.51760.7452.64732.87981.24794.9018-0.4661-0.06480.81930.2234-0.39610.7012-0.7931-0.52160.79960.36740.0942-0.06410.4247-0.06180.5752-24.15912.403391.402
20.70190.09650.26724.2188-2.4561.5959-0.3134-0.85390.19051.0347-0.85620.1819-0.3706-0.35690.58771.9823-0.3225-0.9551-0.0894-0.86820.4492-15.878421.0316115.4995
31.2342.33461.47244.45182.61733.7362-0.2484-0.2820.42060.7889-0.1228-0.7297-0.65010.04750.30780.7922-0.0032-0.40120.3582-0.07150.5651-13.89514.5715104.0515
43.05411.250.95624.720.1694.35820.3897-0.7882-0.2141.4-0.3041-0.14690.5412-0.7421-0.10330.5599-0.1998-0.02080.47740.05140.3019-22.6054-0.9862105.0857
54.26660.03850.14566.211-1.74494.61710.4593-1.5736-0.73151.7767-0.10950.63980.8143-1.2178-0.27281.7726-0.72420.07381.62890.42710.4487-29.5737-12.4602120.7677
61.42021.4471-1.4072.9947-2.75092.54620.2152-0.4593-0.14990.3517-0.70220.3703-0.0297-0.69660.22881.0479-0.3940.38571.8285-0.08161.0886-44.482-7.3898116.0286
71.72760.3781.48832.1956-0.64491.82870.6431-0.9223-0.40490.7755-0.49850.54340.409-0.7333-0.14570.9279-0.54790.00350.91220.15270.5772-32.7686-11.3667102.2716
81.0094-0.36551.33141.0442-0.43265.82940.0147-0.36030.57571.37410.0619-1.2084-0.01150.7382-0.10591.4415-0.0721-0.81260.5335-0.30540.6577-14.902141.114486.7961
93.5490.48920.24654.2972-0.87124.25070.094-0.22720.06451.19870.1659-0.2455-0.21190.1067-0.13450.51340.1617-0.05390.2907-0.0260.3177-25.977532.953779.7922
103.64270.1455-0.41141.09691.87565.41230.2235-0.9911-0.47971.12730.23521.10990.2083-1.453-0.36340.79720.18020.23221.02490.35090.8879-44.395527.700681.4104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 852 through 872 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 873 through 901 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 902 through 957 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 958 through 1081 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 1082 through 1106 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 1107 through 1123 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 1124 through 1160 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 852 through 928 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 929 through 1081 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 1082 through 1160 )B0

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