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- PDB-9s9c: Crystal structure of the apo BRL2 ectodomain from Arabidopsis tha... -

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Basic information

Entry
Database: PDB / ID: 9s9c
TitleCrystal structure of the apo BRL2 ectodomain from Arabidopsis thaliana.
ComponentsSerine/threonine-protein kinase BRI1-like 2
KeywordsMEMBRANE PROTEIN / receptor kinase / steroid receptor / brassinosteroids / leucine-rich repeat
Function / homology
Function and homology information


phloem transport / xylem and phloem pattern formation / leaf vascular tissue pattern formation / brassinosteroid mediated signaling pathway / auxin-activated signaling pathway / transmembrane receptor protein serine/threonine kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / 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 profile. ...: / 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 profile. / 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
Serine/threonine-protein kinase BRI1-like 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsCaregnato, A. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_205201 Switzerland
Citation
Journal: To Be Published
Title: A mechanistic framework for the recognition of chemically diverse brassinosteroids by BRI1-family receptor kinases.
Authors: Caregnato, A. / Chen, H. / Kvasnica, M. / Hohmann, U. / Oklestkova, J. / Ferrer, K. / Broger, L. / Hothorn, L.A. / Strnad, M. / Hothorn, M.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase BRI1-like 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0367
Polymers81,1561
Non-polymers1,8806
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint35 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.613, 118.613, 155.623
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Serine/threonine-protein kinase BRI1-like 2 / BRASSINOSTEROID INSENSITIVE 1-like protein 2 / Protein VASCULAR HIGHWAY 1


Mass: 81155.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Col-0 / Gene: BRL2, VH1, At2g01950, F14H20.2 / Plasmid: pBB2 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9ZPS9, non-specific serine/threonine protein kinase
#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.: 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
#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: 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: obtained synthetically / 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.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.37 Å3/Da / Density % sol: 63.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 23 % PEG 3,350, 0.2 M MgCl2 6H2O, 0.1 M Tris pH 9.0, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999879 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999879 Å / Relative weight: 1
ReflectionResolution: 2.59→47.53 Å / Num. obs: 34843 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 25.2 % / Biso Wilson estimate: 91.4 Å2 / CC1/2: 1 / Rrim(I) all: 0.11 / Net I/σ(I): 20.3
Reflection shellResolution: 2.59→2.76 Å / Redundancy: 21.3 % / Mean I/σ(I) obs: 1.53 / Num. unique obs: 5378 / CC1/2: 0.592 / Rrim(I) all: 2.373 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→47.53 Å / SU ML: 0.4898 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.6051
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2919 1741 5 %
Rwork0.2674 33102 -
obs0.2687 34843 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 133.16 Å2
Refinement stepCycle: LAST / Resolution: 2.59→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 122 10 5100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00415186
X-RAY DIFFRACTIONf_angle_d0.65987058
X-RAY DIFFRACTIONf_chiral_restr0.0441855
X-RAY DIFFRACTIONf_plane_restr0.0041905
X-RAY DIFFRACTIONf_dihedral_angle_d12.07492042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.670.53791290.60742465X-RAY DIFFRACTION90.67
2.67-2.750.38631440.4382752X-RAY DIFFRACTION99.59
2.75-2.850.3631440.37652715X-RAY DIFFRACTION99.37
2.85-2.960.36681450.36872741X-RAY DIFFRACTION99.55
2.96-3.10.38621440.34962725X-RAY DIFFRACTION99.38
3.1-3.260.30961430.3552735X-RAY DIFFRACTION99.41
3.26-3.470.3321460.30612782X-RAY DIFFRACTION99.86
3.47-3.730.30871450.25322749X-RAY DIFFRACTION99.42
3.73-4.110.29541460.24612787X-RAY DIFFRACTION99.76
4.11-4.70.2471460.20592798X-RAY DIFFRACTION99.83
4.71-5.920.25891510.25732855X-RAY DIFFRACTION99.83
5.93-47.530.28571580.25672998X-RAY DIFFRACTION99.84
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)
13.066287092150.431527270932-2.328429989923.539937178780.109655028135.36745965851-1.56415310672-1.97753892291-0.220527824190.55870651988-0.64641395761-0.111967517576-1.709696467621.772980484191.417602616141.620918079230.33814657487-0.6828467149622.59151742871-0.09855587606251.44048978436-16.5452599352.3908014885511.6322636625
23.26960831960.2999958856110.8558162729621.62147718570.08015276226235.35927007768-0.0416487819841-0.567743978919-0.209420554290.3080529746140.104072818438-0.3378792776850.5397584456340.833021084817-0.1522435149791.067293004550.252522974654-0.0506432145631.002850418320.04254947129160.779755698161-39.0395888506-5.70011237709-4.84767639972
33.939985745251.58607794822-2.676870795243.65517749904-3.162999812567.03920042272-0.2039978762930.2100756085290.125419547507-0.2304290908490.3276695390270.2034654336820.255501802078-0.156219737089-0.198894057180.7645839611630.0177596777929-0.04256377101540.7045429630110.001315655050630.645119993076-46.446605447910.4455719476-38.4983345575
45.626607006410.694301892776-2.752153513795.45058300634-3.122355645617.08025244472-0.04304299689360.6084091367840.390657964326-0.56979303524-0.250132953320.1933635098190.6580126992460.5380329799940.1388545823651.01646995092-0.1599122347790.1561791045431.055885889820.06203716453970.850714872207-28.504125412217.0093182518-54.3283523963
50.1791218467571.091271181570.5236304164612.05068914630.2874268216012.08348993189-0.6764393856780.417257014078-0.386874930495-0.9300677742990.429196186422-0.581409602369-0.4130545839020.226939469398-0.1149081601451.30877209261-0.1016864055380.3026777809971.24654486111-0.01140099712881.17845737295-14.287177593516.5229063985-51.9665724351
63.79953043421.384312357280.1680955255482.270259260770.9947659558063.87943933802-0.2772004422960.693493556737-0.923645551915-0.603679748107-0.168048927099-0.2698925849510.795452932909-0.2984959955820.160629950691.18717463219-0.03123277607710.3641801319391.07878520721-0.0865261210751.1564288735-10.29578851768.45892648665-55.2557352145
72.648665684940.313790008444-1.415695908731.97055904916-0.3645078944944.27292283025-0.4425873355460.510732367132-1.23811092444-2.087955112080.422045888156-0.8936173385290.4941945133151.337481591760.7048535728121.78933662049-0.01999506749810.5583116544661.42887571709-0.2759468384111.66550503164-6.17037395271-2.77259311409-59.4561570795
82.464432740040.212660801236-2.656537926356.21572081364-0.6619217582362.75906636337-1.236567750230.78123881697-1.26657750385-2.176452439790.09817848982440.1138940723923.156803850460.8368118577830.6948716841922.027092845990.2419545101880.90021673671.33635876207-0.2479533971121.64096642346-8.23907496071-10.4714526669-64.0999722064
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 33 through 72 )33 - 721 - 40
22chain 'A' and (resid 73 through 283 )73 - 28341 - 251
33chain 'A' and (resid 284 through 453 )284 - 453252 - 421
44chain 'A' and (resid 454 through 501 )454 - 501422 - 469
55chain 'A' and (resid 502 through 572 )502 - 572470 - 532
66chain 'A' and (resid 573 through 652 )573 - 652533 - 587
77chain 'A' and (resid 653 through 686 )653 - 686588 - 621
88chain 'A' and (resid 687 through 715 )687 - 715622 - 650

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