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- PDB-9qrs: Crystal structure of CERK6 extracellular domain -

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Basic information

Entry
Database: PDB / ID: 9qrs
TitleCrystal structure of CERK6 extracellular domain
ComponentsLysM type receptor kinase
KeywordsPLANT PROTEIN / LysM / Chitin / receptor
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
alpha-D-mannopyranose / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesLotus japonicus (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsCheng, J.X.J. / Gysel, K. / Stougaard, J. / Andersen, K.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF79 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
DepositionApr 4, 2025Deposition 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
B: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,15613
Polymers44,7592
Non-polymers4,39611
Water6,593366
1
A: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3047
Polymers22,3801
Non-polymers1,9246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LysM type receptor kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8526
Polymers22,3801
Non-polymers2,4725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.290, 131.580, 53.900
Angle α, β, γ (deg.)90.000, 108.137, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein LysM type receptor kinase


Mass: 22379.723 Da / Num. of mol.: 2
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

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Sugars , 7 types, 9 molecules

#2: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-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
DManpb1-3DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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.: 2 / 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
#9: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 368 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.49 Å3/Da / Density % sol: 64.71 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 28% (w/v) PEG-2000 monomethyl ether

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.86→43.99 Å / Num. obs: 49236 / % possible obs: 97.36 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.66 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.03796 / Rpim(I) all: 0.01571 / Rrim(I) all: 0.04115 / Net I/σ(I): 23.5
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.9937 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 2433 / CC1/2: 0.511 / Rpim(I) all: 0.5522 / Rrim(I) all: 1.147 / % possible all: 67.79

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→43.99 Å / SU ML: 0.2718 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.4173
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1963 2000 4.06 %
Rwork0.175 47232 -
obs0.1759 49232 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.79 Å2
Refinement stepCycle: LAST / Resolution: 1.87→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 290 366 3694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533404
X-RAY DIFFRACTIONf_angle_d0.93184640
X-RAY DIFFRACTIONf_chiral_restr0.0651587
X-RAY DIFFRACTIONf_plane_restr0.0049577
X-RAY DIFFRACTIONf_dihedral_angle_d17.9761507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.4622980.44282356X-RAY DIFFRACTION67.79
1.92-1.970.37931430.3393344X-RAY DIFFRACTION97.05
1.97-2.030.29531460.26293461X-RAY DIFFRACTION99.7
2.03-2.090.22731460.22053438X-RAY DIFFRACTION99.83
2.09-2.170.21181450.19253431X-RAY DIFFRACTION99.83
2.17-2.250.2091470.2053471X-RAY DIFFRACTION99.83
2.25-2.360.25111450.19423440X-RAY DIFFRACTION99.83
2.36-2.480.23251470.20433452X-RAY DIFFRACTION99.94
2.48-2.630.19881460.18123456X-RAY DIFFRACTION99.94
2.63-2.840.18921470.19223472X-RAY DIFFRACTION99.89
2.84-3.120.2551480.19583469X-RAY DIFFRACTION99.89
3.12-3.580.2081470.17373465X-RAY DIFFRACTION99.94
3.58-4.50.14381460.14373475X-RAY DIFFRACTION99.89
4.5-43.990.15571490.13553502X-RAY DIFFRACTION99.81
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)
17.69510625451-4.614284499755.579194747136.50905073627-5.746782697979.472895585320.2634123628080.105400942744-0.4331422224050.1982423258560.173450533549-0.05462985053120.1141474109150.137360785573-0.5024217060460.295785779424-0.00484814065976-0.02520938995650.252423801778-0.05934260417490.317617553392-3.98822509389-15.905410749418.0522752862
26.983935408-2.528863691971.689779816242.781699376170.2117149166344.19915573496-0.120554710618-0.3106579514140.1837255495190.7435442200280.352534833542-1.72431527885-0.006887365402580.8420900409650.08026697200590.3667175552340.0399297031897-0.1924015408680.409447975921-0.07767256555980.5728155564969.68725094484-17.933725360124.6834064849
35.84477431051-0.327417224121.383168503744.71862366912-1.501862952053.788661471280.0606459680398-0.4543602697040.03447240809890.833133824561-0.0272812414666-0.614577074127-0.4416923256170.433080977373-0.125503047590.3662874766860.034409632997-0.1272314164740.286441936907-0.06757342184690.3621428875772.5364263993-15.943543832925.7515361367
42.53901190866-1.7266442243-1.462300068585.878279673550.6839296643413.03921039660.02655226208570.0602876764956-0.412868427264-0.158422507985-0.0631374575701-0.2127900623190.5593594480710.1181060045390.0770335649270.3867854508460.0702475271681-0.06513719574950.285810577524-0.04852609258690.3964711143072.72394013194-32.014771734215.8826951035
55.22395774783-1.72990560658-2.384693965913.509042402780.8223868336274.00992410724-0.0624522463648-0.267638941568-0.1767754690740.3560702812230.06982998016540.1219381815070.0621880954739-0.1050603780770.002329650734330.249679288169-0.0196850082518-0.02661528442920.258639383358-0.01604001989150.202743077995-11.300510115-17.210272306325.0818731448
63.77238055948-2.731233392185.258946186982.33600847915-4.028881104077.98752167924-0.124533914286-0.01539400683340.6355569636970.309344828597-0.133486225495-0.897391433816-0.9328171577540.2226659797510.3283568964520.511377198258-0.0167749406374-0.009073878444320.340562272321-0.05148910684420.459256919088-3.57250358032-3.5430530028224.8178841265
75.405462391441.789580843685.528037878720.8830016679531.777725485525.66210995222-0.229197840382-0.0930467556990.258574310760.132012659491-0.01716790144120.01492515011120.4113308987560.1423814483780.1565304139791.593501227220.01026487215230.02927524281171.389032185170.1748046107880.598169825104-10.72617775963.551008685414.1793301962
84.270385260490.304175172228-1.406029323814.19541163131-5.434512842487.79288225014-0.06295312870730.1373995448620.365254486603-0.1396472968930.04139887575290.0730818613285-0.1572400445950.15115419982-0.06159924450970.389102070391-0.0624420832444-0.02735946973080.239679035914-0.04388975783170.261549622172-10.13008700845.36673589374-1.18091680441
92.990818744070.728746645499-0.3525039245057.50876774034-3.474082458214.538552168260.134925892693-0.1485698404260.5209751401420.746955092743-0.27859250919-0.156942503785-0.9913374543590.4169638745730.09549659014290.456968108952-0.085619519088-0.02556368806210.287663585664-0.008122047119820.364688420731-5.043615668111.7237624717-0.141261350196
102.39801225052-1.05707124912-0.7483175700051.127660905941.07977111091.70916454758-0.0513103393078-0.01316667515340.3066934240071.003991094960.4584098516261.65294009923-1.02819741885-0.545748831958-0.2633483530550.73816132440.1923862695050.311558643360.43215090110.1228286976770.919879050496-23.025549855512.46630592931.82992065831
112.88863520211-0.6340243987561.201789393255.50689614249-1.255740465325.68466971383-0.03041342850680.2418548205430.0714945099578-0.248079739015-0.0233225369976-0.0573091496964-0.005300495122460.2458335582190.01460955338790.230596335894-0.01860555701960.01928159053790.330839473707-0.004676409162470.23427767451-7.09777941105-3.79567607631-7.97551437718
120.2371803146190.021905261882-0.1318784035140.00271252709396-0.01407852592620.07454369858630.007541399405330.0703622849716-0.0822297966088-0.07498482729560.0457968984531-0.02599104236790.0681103165569-0.0840476949413-0.002980149727092.106626424540.28264814451-0.337460244441.3427204362-0.06305535476391.942068066065.01844013131-15.97077125127.12182874062
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 26 through 41 )AA26 - 411 - 16
22chain 'A' and (resid 42 through 68 )AA42 - 6817 - 43
33chain 'A' and (resid 69 through 97 )AA69 - 9744 - 72
44chain 'A' and (resid 98 through 145 )AA98 - 14573 - 120
55chain 'A' and (resid 146 through 210 )AA146 - 210121 - 185
66chain 'A' and (resid 211 through 221 )AA211 - 221186 - 196
77chain 'A' and (resid 222 through 223 )AA222 - 223197 - 198
88chain 'B' and (resid 26 through 46 )BL26 - 461 - 21
99chain 'B' and (resid 47 through 97 )BL47 - 9722 - 72
1010chain 'B' and (resid 98 through 152 )BL98 - 15273 - 127
1111chain 'B' and (resid 153 through 222 )BL153 - 222128 - 197
1212chain 'B' and (resid 223 through 224 )BL223 - 224198 - 199

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