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- PDB-9h3b: Lotus japonicus CERK6 extracellular domain in complex with chitop... -

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Basic information

Entry
Database: PDB / ID: 9h3b
TitleLotus japonicus CERK6 extracellular domain in complex with chitopentaose
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / LysM / chitin receptor / carbohydrate
Function / homology
Function and homology information


transmembrane receptor protein kinase activity / non-specific serine/threonine protein kinase / innate immune response / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
LysM domain / LysM domain receptor kinase CERK1/LYK3-like / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. ...LysM domain / LysM domain receptor kinase CERK1/LYK3-like / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsHansen, S.B. / Gysel, K. / Andersen, K.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
The Carlsberg FoundationCF21-0139 Denmark
Danish Council for Independent Research3103-00137B Denmark
Novo Nordisk FoundationNNF21OC0071300 Denmark
CitationJournal: To Be Published
Title: Structural basis for size-selective perception of chitin in plants
Authors: Gysel, K. / Hansen, S.B. / Ruebsam, H. / Alsarraf, H.M.A.B. / Madland, E. / Cheng, J.X.J. / Baadegaard, C. / Poulsen, E.C. / Vinther, M. / Fort, S. / Stougaard, J. / Andersen, K.R.
History
DepositionOct 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 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: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9305
Polymers22,5181
Non-polymers2,4124
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint41 kcal/mol
Surface area11360 Å2
Unit cell
Length a, b, c (Å)60.137, 60.137, 390.422
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein LysM type receptor kinase


Mass: 22517.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lotus japonicus (plant) / Gene: LYS6 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3KTZ6
#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(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.: 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
#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: 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


Type: oligosaccharide / Mass: 1033.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
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: 4.53 Å3/Da / Density % sol: 72.82 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Potassium sodium tartrate tetrahydrate 0.1M Bis-Tris propane pH 6.5 18% 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: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.58→19.68 Å / Num. obs: 5787 / % possible obs: 40.6 % / Redundancy: 22 % / Biso Wilson estimate: 84.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.029 / Rrim(I) all: 0.132 / Net I/σ(I): 13.4
Reflection shellResolution: 2.58→2.914 Å / Rmerge(I) obs: 6.308 / Num. unique obs: 289 / CC1/2: 0.434 / Rpim(I) all: 1.317 / Rrim(I) all: 6.45

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→19.68 Å / SU ML: 0.2599 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.4394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2694 270 5.01 %
Rwork0.2504 5122 -
obs0.2514 5392 37.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 110.49 Å2
Refinement stepCycle: LAST / Resolution: 2.58→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 162 0 1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421719
X-RAY DIFFRACTIONf_angle_d0.95212344
X-RAY DIFFRACTIONf_chiral_restr0.0492297
X-RAY DIFFRACTIONf_plane_restr0.0051291
X-RAY DIFFRACTIONf_dihedral_angle_d16.3139806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-3.250.3857320.4226609X-RAY DIFFRACTION9.31
3.25-19.680.26592380.24594513X-RAY DIFFRACTION64.58
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)
12.235470072162.01917699883-0.2466473727514.62746821353-1.748902419760.8716801682720.47277941101-0.6203967929950.8802616097870.8494914328790.2115423778270.150109037190.8912626496131.23983981848-0.6176169342530.3431591391450.24429502458-0.2274824418821.33960767371-0.3980114443350.579974871905-19.138326554415.945426202-16.0004102103
22.788916973591.292307602891.511586110191.95006160312-1.216293995173.536192269540.5185984439140.3146095827640.943859206326-0.3232549550770.2841764249470.128150366504-0.06389967997410.191467859454-0.2539915849910.7463569772970.30234788644-0.1492453649111.32285767455-0.6515236710141.03873850012-23.2597697127.0035790802-14.5390761244
32.565487617090.355886241283-0.6814463633755.43299300181-0.1149803196842.88538164330.260342756175-0.3933471993110.229214364454-0.459349943377-1.10231451515-1.167009982961.30576134094-0.7969484612060.7084635836430.9040128615420.1020728811220.1879906364011.16846061705-0.4683414048511.04663548978-32.520146090620.5963402595-10.5181868691
40.6110331214650.6021922941340.3934290014246.066381147372.16039885440.827578223894-0.0257089821962-1.865280260220.01039664208541.43949432586-0.1604247804950.7401785792360.129697858303-0.608087047002-0.1158231871370.5826044990160.1351536276560.08363238794381.59127801979-0.3381341697840.832930486295-24.637706937215.9712034138-9.02984344353
51.20554970311-1.81023675155-0.05368075945718.65627691945-2.483168636353.852939841680.1619204154740.316997124130.32139756759-0.8046385037020.0959115064886-1.41498537726-0.0908400779630.853998286483-1.359052366250.7745734878250.441536149108-0.06392935067161.14517842468-0.5026896466370.78629933725-12.460371058318.1677884009-25.503043246
61.149178787271.761540373510.5886794664623.321861710291.636507325441.16561752084-0.390602589984-0.9673133728441.065887965231.8063585842-0.617509864455-0.30030561351-1.033680042720.756624041870.8370345618371.305992079810.15486395294-0.4558459568732.03698633272-0.7437316477031.23817188768-9.3922836753830.8543991395-8.33724452523
71.868106332332.58011939635-3.101643399286.83031674339-4.09051129015.16860736254-0.449934566618-0.00478503586526-0.4225859544660.267489607970.366972784982-0.8062542400970.6604205051521.41191963673-3.037215354140.6472842201910.343763703484-0.1121154267111.48853630725-0.8203572380490.445353745689-7.5317306197120.0196675762-11.6674254809
88.705236488157.590514465640.6052247737216.677398754010.5417063517657.6894246590.289930786439-0.3553506022872.12581222311-0.109261445429-0.02842565038070.7646865007311.087162516811.09679632556-0.2296257127150.850204774056-0.00221522746729-0.2181411779451.31364981018-0.4662243150941.0717585244-2.4187014751130.9415142751-12.8946690506
92.76799150641-0.353273298307-0.03115606764834.41224666320.3949222136566.594075526730.5401551361760.377742826353-0.309428615587-0.492718842563-0.51449123402-0.3220878454231.19485242035-0.4152249855130.1359362160670.6350467728250.525449625826-0.1035685764021.02206627793-0.2216698100470.492743508438-18.89181117397.99672386221-23.7009104989
105.381404503633.626030143914.915863015072.441121900793.311526631634.488608011180.70805086937-1.75744032301-0.9172128019970.371966150645-0.3928569617770.1587248441071.65505832291-0.168588821904-0.7630066227450.8798433003760.403275112283-0.1887119103031.17399164634-0.05347859281480.575740060234-17.80658102327.60501353835-9.19881890861
116.584846790971.501123745392.681531783040.63508731904-0.02884112080932.490829421981.10058302732-0.400094746352-2.028638303330.6796271274370.1303872338580.143847708781.048316857310.354411162142-0.2292990971852.620501111390.411906123826-0.2825319297891.05241401831-0.1366445290981.16519588769-22.621254403-0.675057944645-13.0759034728
124.03295064094-1.58772163084.596093911235.69697856215-5.368685844131.99979104258-0.3651569500660.133450659505-0.316831497552-0.02866564256690.395532111704-0.8455647505221.122177185611.656980653530.4316202155481.197559862440.319887497315-0.3724939096640.67161483665-0.5846488719220.641999248517-13.77075265043.37537853282-12.8724612717
131.66689328205-0.424611250369-0.8804913447433.213736595770.8049579845182.7844260922-0.253440376053-0.223662885526-0.1226111879911.206410754741.01949808601-0.009810438523710.06560581118960.358117510443-0.8562660738321.766499668070.04382741677870.03671805907990.74772243716-0.1870545336740.776426144442-31.34790298789.06793113453-22.4102983795
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 26 through 46 )26 - 461 - 21
22chain 'A' and (resid 47 through 61 )47 - 6122 - 36
33chain 'A' and (resid 62 through 79 )62 - 7937 - 54
44chain 'A' and (resid 80 through 89 )80 - 8955 - 64
55chain 'A' and (resid 90 through 103 )90 - 10365 - 78
66chain 'A' and (resid 104 through 112 )104 - 11279 - 87
77chain 'A' and (resid 113 through 133 )113 - 13388 - 108
88chain 'A' and (resid 134 through 148 )134 - 148109 - 123
99chain 'A' and (resid 149 through 165 )149 - 165124 - 140
1010chain 'A' and (resid 166 through 176 )166 - 176141 - 151
1111chain 'A' and (resid 177 through 194 )177 - 194152 - 169
1212chain 'A' and (resid 195 through 210 )195 - 210170 - 185
1313chain 'A' and (resid 211 through 222 )211 - 222186 - 197

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