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- PDB-28tf: Crystal structure of Lotus japonicus CHIP13 ectodomain in complex... -

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Basic information

Entry
Database: PDB / ID: 28tf
TitleCrystal structure of Lotus japonicus CHIP13 ectodomain in complex with chitoheptaose
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / LysM / Chitin / Plant immunity
Function / homology
Function and homology information


response to other organism / protein kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / : / NFP/LYK LysM1 domain / LYK4/5 LysM3 domain / : / : / LYK3/4/5 LysM2 domain / Lysin motif / LysM domain profile. / LysM domain ...: / : / NFP/LYK LysM1 domain / LYK4/5 LysM3 domain / : / : / LYK3/4/5 LysM2 domain / Lysin motif / LysM domain profile. / LysM domain / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-glucopyranose / LysM type receptor kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsGysel, K. / Andersen, K.
Funding support Denmark, 4items
OrganizationGrant numberCountry
The Carlsberg FoundationCF21-0139 Denmark
Danish Council for Independent Research3103-00137B Denmark
Novo Nordisk FoundationNNF210C0071300 Denmark
Danish National Research Foundation Denmark
CitationJournal: Science / Year: 2026
Title: Structural basis for size-selective chitin perception in plants
Authors: Gysel, K. / Hansen, S.B. / Ruebsam, H. / Andersen, K.
History
DepositionFeb 18, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,65910
Polymers25,0091
Non-polymers3,6509
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint73 kcal/mol
Surface area10970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.453, 45.030, 76.641
Angle α, β, γ (deg.)90.000, 102.986, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

21A-670-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein LysM type receptor kinase


Mass: 25008.721 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Gene: LYS13 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3KU00

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Sugars , 5 types, 6 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}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.: 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
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1440.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}}}}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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#7: Sugar ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-D-glucosamine / 2-acetamido-2-deoxy-alpha-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 364 molecules

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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 6.5 25% w/v PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.71 Å
DetectorType: DECTRIS EIGER2 X CdTe 16M / Detector: PIXEL / Date: Sep 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 1.15→33.11 Å / Num. obs: 94665 / % possible obs: 99.52 % / Redundancy: 6.8 % / Biso Wilson estimate: 19.06 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06589 / Rpim(I) all: 0.02708 / Rrim(I) all: 0.07134 / Net I/σ(I): 9.3
Reflection shellResolution: 1.15→1.16 Å / Rmerge(I) obs: 2.817 / Mean I/σ(I) obs: 0.42 / Num. unique obs: 2876 / CC1/2: 0.166 / Rpim(I) all: 1.326 / Rrim(I) all: 3.127

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→33.11 Å / SU ML: 0.2243 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 29.2672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 4702 4.97 %
Rwork0.1575 89862 -
obs0.1589 94564 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.68 Å2
Refinement stepCycle: LAST / Resolution: 1.15→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 245 361 2340
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01012125
X-RAY DIFFRACTIONf_angle_d1.2282917
X-RAY DIFFRACTIONf_chiral_restr0.1845389
X-RAY DIFFRACTIONf_plane_restr0.0084356
X-RAY DIFFRACTIONf_dihedral_angle_d15.23351052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.50391360.50152733X-RAY DIFFRACTION92.31
1.16-1.180.53241480.50362901X-RAY DIFFRACTION96.92
1.18-1.190.4971660.47022985X-RAY DIFFRACTION99.78
1.19-1.210.42191440.4592978X-RAY DIFFRACTION99.74
1.21-1.220.54751430.49133040X-RAY DIFFRACTION99.75
1.22-1.240.47811650.49762957X-RAY DIFFRACTION99.78
1.24-1.260.49011620.4442991X-RAY DIFFRACTION99.65
1.26-1.270.44311530.39582988X-RAY DIFFRACTION99.65
1.27-1.290.36511610.36112962X-RAY DIFFRACTION99.81
1.29-1.320.34831500.30343026X-RAY DIFFRACTION99.78
1.32-1.340.32431500.28672963X-RAY DIFFRACTION99.9
1.34-1.360.30941700.25543028X-RAY DIFFRACTION99.91
1.36-1.390.28071570.22892998X-RAY DIFFRACTION99.94
1.39-1.420.24761590.20992971X-RAY DIFFRACTION99.84
1.42-1.450.23021590.20543014X-RAY DIFFRACTION99.91
1.45-1.480.23371690.20142986X-RAY DIFFRACTION99.94
1.48-1.520.25821570.18992980X-RAY DIFFRACTION99.94
1.52-1.560.19891560.14553041X-RAY DIFFRACTION99.97
1.56-1.610.18871480.14122984X-RAY DIFFRACTION100
1.61-1.660.17121420.12793041X-RAY DIFFRACTION99.94
1.66-1.720.20011590.12712991X-RAY DIFFRACTION99.97
1.72-1.790.1861640.12913013X-RAY DIFFRACTION99.91
1.79-1.870.17311710.13082991X-RAY DIFFRACTION99.94
1.87-1.970.18221440.12963046X-RAY DIFFRACTION99.97
1.97-2.090.13111700.1222998X-RAY DIFFRACTION100
2.09-2.250.13881640.12333020X-RAY DIFFRACTION100
2.25-2.480.14751610.12813021X-RAY DIFFRACTION100
2.48-2.830.16061760.13553027X-RAY DIFFRACTION99.97
2.83-3.570.14761470.13953073X-RAY DIFFRACTION99.97
3.57-33.110.18231510.14793115X-RAY DIFFRACTION99.24

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