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- PDB-9h6v: Lotus japonicus CERK6 extracellular domain in complex with two na... -

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Basic information

Entry
Database: PDB / ID: 9h6v
TitleLotus japonicus CERK6 extracellular domain in complex with two nanobodies
Components
  • LysM type receptor kinase
  • Nb-aCERK6-1
  • Nb-aCERK6-2
KeywordsPLANT PROTEIN / chitin receptor / LysM / nanobody
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)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsGysel, K. / Alsarraf, H.M.A.B. / Hansen, S.B. / Andersen, K.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
The Carlsberg FoundationCF21-0139 Denmark
Danish Agency for Science Technology and Innovation3103-00137B 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 25, 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
B: LysM type receptor kinase
E: Nb-aCERK6-2
F: Nb-aCERK6-2
D: Nb-aCERK6-1
C: Nb-aCERK6-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,03823
Polymers104,1006
Non-polymers2,93817
Water2,684149
1
A: LysM type receptor kinase
F: Nb-aCERK6-2
C: Nb-aCERK6-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,58911
Polymers52,0503
Non-polymers1,5398
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LysM type receptor kinase
E: Nb-aCERK6-2
D: Nb-aCERK6-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,44812
Polymers52,0503
Non-polymers1,3989
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.280, 57.580, 86.810
Angle α, β, γ (deg.)96.972, 88.981, 96.418
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D3KTZ6

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Antibody , 2 types, 4 molecules EFDC

#2: Antibody Nb-aCERK6-2


Mass: 14955.765 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody Nb-aCERK6-1


Mass: 14714.392 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Sugars , 2 types, 8 molecules

#4: 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.: 3
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
#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.: 5
Source method: isolated from a genetically manipulated source
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

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Non-polymers , 2 types, 158 molecules

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


Mass: 62.068 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion / Details: 0.2 M sodium bromide 20 % 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: 0.97 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Oct 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.186→48.971 Å / Num. obs: 25361 / % possible obs: 52 % / Redundancy: 7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.092 / Rrim(I) all: 0.244 / Net I/σ(I): 8.2
Reflection shellResolution: 2.186→2.506 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1269 / CC1/2: 0.187 / Rpim(I) all: 0.647 / Rrim(I) all: 1.684 / % possible all: 7.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→32.42 Å / SU ML: 0.3077 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 34.6908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 1259 4.97 %
Rwork0.2044 24080 -
obs0.2068 25339 51.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.23 Å2
Refinement stepCycle: LAST / Resolution: 2.19→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6783 0 190 149 7122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197108
X-RAY DIFFRACTIONf_angle_d0.48719635
X-RAY DIFFRACTIONf_chiral_restr0.04061092
X-RAY DIFFRACTIONf_plane_restr0.00411239
X-RAY DIFFRACTIONf_dihedral_angle_d11.09772725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.270.442930.439160X-RAY DIFFRACTION1.18
2.27-2.380.3683160.3937305X-RAY DIFFRACTION6.02
2.38-2.50.3123340.3639816X-RAY DIFFRACTION15.65
2.5-2.660.3324910.35641679X-RAY DIFFRACTION32.88
2.66-2.860.39661360.33612582X-RAY DIFFRACTION50.18
2.86-3.150.35761910.28463648X-RAY DIFFRACTION71.07
3.15-3.610.3082490.22814771X-RAY DIFFRACTION92.72
3.61-4.540.21842700.16965114X-RAY DIFFRACTION99.52
4.54-32.420.1942690.15775105X-RAY DIFFRACTION99.21
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)
13.82149085856-0.6416974086211.105127422034.11016588392-1.538424074812.602355731090.145503161478-0.443701259089-0.1708123352330.180125621819-0.005850897155110.0585741346593-0.391298313340.0305480082788-0.1063340045340.292017013329-0.116928917627-0.0249547458640.2532524382150.002678852059270.139215285902-1.59912206026-8.65275238162-2.68000361568
24.06663066046-1.97049750165-5.118247317655.209146601181.852775856377.4902579505-0.06501167555940.2239695418240.985595602687-0.233868381996-0.1868556196730.0486373096416-1.16716936483-0.205687319464-0.127354989230.805880896733-0.0110406871704-0.1875171938340.3874416197540.08617030852150.393480695181-3.943341662230.495738447346-16.0877519788
37.425383649880.298992091394-0.01475871550873.803905821580.8172833548672.19719924270.170553028129-0.3519751932241.62977620680.1293505539850.046964758515-0.324814744116-2.034436298940.137913246245-0.1866463742091.0502368887-0.127659294105-0.08804599513250.378426949125-0.1025350097150.649288679621-3.988415995668.63013909161-4.99576728208
44.051304737541.400865113081.430092054.807652023740.3160232504910.5106824734110.038588645285-0.3467867404711.658195865450.73386921073-0.364345175245-0.0674418558811-1.20655187008-0.5363977579960.1494360519251.138041790030.14369924006-0.1407374739590.37547216458-0.03339770489530.612431126096-10.196980284311.1036292942-8.48571194892
51.87432185652-1.15684403137-0.6899818551262.193030829190.3842169579581.96375337576-0.132958983211-0.3149154439150.402461729095-0.261577129824-0.229516744038-0.746745141151-0.4765043751770.6520353752950.03790021602170.307703970802-0.3524551467390.01646595069350.5472794103540.225920623880.31014847770213.2331567352-6.8450747637-9.50176036449
66.46939004018-0.272823440959-0.04797171072098.728548074230.08139047829893.48613710899-0.1359573255240.0717909072702-0.998171891949-0.8398125060280.1162176533640.1011553067061.24510672566-0.1572397934-0.1560798102280.794975462844-0.1217657935580.1609634930740.2135984009210.07922931082920.66453794499415.433550229516.6260503507-47.1993191421
71.71602441506-0.345978036701-0.6694642635791.69383540213-1.02527062371.086582630780.01516732503910.0858308217852-1.04341688525-0.434590850467-0.1850290979840.1788107685361.42912461505-0.742375347672-0.05493997352070.87593321363-0.2761715899640.01484969153570.2743476466770.00667396255390.65372659547612.300310082714.0890329158-48.7112300371
87.381853257042.413231335811.185950632786.222089379480.9652779171071.749670361020.295519535472-0.456045171999-1.472017566070.530605559287-0.3415894641920.5641194270041.51432182074-0.602019621216-0.2666453728021.10153667161-0.3178623381410.008676338758260.5236532733190.05303349571050.70173212032112.9069521318.19131700056-41.6505412815
92.61583621068-0.1447267944550.5249737681244.350006202160.3695163279821.907149344810.1489031226880.061282894073-0.902962157844-0.549284870393-0.315214385307-0.5643233925160.8778965607540.4735634485390.009279264680460.6925321980530.2497150061030.0388476235480.2622491137150.2968586203820.4887193976129.284829626616.664559221-46.0399728052
103.817865008990.407229741509-1.850096180515.33974915968-1.162503735357.62681579598-0.612579016769-0.4292228973820.135620708755-0.5166808488470.212046852141-0.625240434583-0.9852420366261.219915739070.3377915274940.928983980585-0.4414202668250.08582583891840.728179790456-0.157449909970.91382577884735.026826110548.8862976891-35.1924755461
116.32434985455-0.1867893702184.125227769348.867689171343.830084861294.567518057950.103507196227-0.5570388925540.05423808999220.4082071123450.000407456518965-1.07075630258-0.1649543121310.582867277170.02458250437420.433111845707-0.2355581491150.001681159914740.517107570453-0.0961669181370.4689756315637.004171598937.0346878607-35.3545051356
125.17241749598-3.062087712950.1572650374447.802404740664.469649840683.479416048250.112924466639-0.4346863479750.249058095606-0.2599718625780.2542101431320.241124414741-0.201635909450.255115485548-0.4900133807810.596810854071-0.1820397310830.09536263870920.527172819891-0.08123372067920.28664858734128.502153229341.4861975697-38.035803024
136.012938981040.320959793267-0.8737154844685.161079160313.647663980345.73313340449-0.0420044645835-0.4677824599650.121960073090.502939387610.770267570683-1.37938337579-0.2398628083221.47648683235-0.765878329910.511431039356-0.147988910687-0.194328113420.783516855712-0.1085615204850.35026341071738.962215607236.8840034993-32.9583074
143.90054568533-2.73580723424-3.919013658718.781833539120.08002361651764.9747643005-0.04681547962021.08279802937-0.91480834511-0.74344633342-0.01207459217670.294870229440.9112434738651.116301668190.4103227545660.9056938650860.40952870303-0.07382273815370.779325424332-0.1732024728290.41301571671216.8429889894-39.8758840519-18.5061455902
150.503897242786-0.318128701971-0.8952220002112.868693751422.064599422662.436816571710.6978719162440.625201667684-0.4572715494650.0288531406807-0.388880293489-0.2861045576640.9027718226430.724568997295-0.1908151160270.4978585857450.276532920905-0.1047983200560.8119537003380.001205388072310.27445066852317.5983665543-29.1640763049-14.3732250654
166.481556714844.940770017414.266125502144.219186365563.540004562633.84460183298-0.8629995144150.7186675335030.950104374812-0.409071952827-0.2743283908592.00840428208-1.33947937845-0.1759349657860.7807084707080.8167376611430.41815128339-0.2348873758561.23995929541-0.04642734703640.8005153670585.18434408373-25.5958146387-21.0098106001
174.88871553563-0.01882970803770.6616693239895.992502861571.134735957582.245173784050.1165766887181.29909431209-0.237710595664-0.341953626146-0.0891222603607-0.1561453979370.3168216142020.949419339348-0.03297657616560.4613148075090.279277145817-0.02106473178420.9796086984390.1199635577160.38242984086416.5573575456-31.0737415445-17.7919426417
183.010575661210.382821922220.4030248756412.4257122812-1.631073849354.80409198918-0.07726590817160.02163296080160.6264210192230.156101650291-0.394628914574-0.416834702309-0.366813022883-0.0135274461482-0.8013457098120.3116965199860.08657423462530.0710503716150.1264266889480.02797689830220.30108604898816.691479291749.3626336707-68.0537400664
191.740351557540.990231851303-1.573236434040.887444667534-0.5732520088471.7414942801-0.473729162879-1.085693475061.118657119081.004096842440.2951299859950.908738315301-1.03490356106-0.947745622115-0.1590862041210.5934024521340.3716962091310.105254347431.04471747195-0.062565751410.77706426472311.991379713441.0260715845-50.6177810426
203.646094330970.437823440759-0.5313369337512.26360023157-1.220012552811.805885967320.03831219390380.341665429490.230332970934-0.05226883343930.213833791236-0.0375615419186-0.1510164186690.00636707282407-0.146280587042-0.188009209355-0.005557438818510.0469812546860.3004258240740.02683486468150.1375940859516.824054441939.3972344341-67.1936821086
214.67430059613-0.3526288068822.444304840223.11005697126-0.6207967693486.40553864419-0.1349173070450.091235696195-0.226407506521-0.280897690907-0.384942941739-0.5128658802160.6331894034990.431627008547-1.65373453840.212874623446-0.03315682178970.02833348197460.144495114660.2659317392170.310522470046-1.5327216432-37.331401939816.209426078
226.677897752590.228840967046-1.367605626775.28242045502-1.718713454511.349618250720.1423789175211.02762542690.00709551885595-1.24117251336-0.6770855000830.3407465154270.3934189373560.1047602857840.7533068037290.3478940301510.0983567680139-0.112777609150.33586707637-0.1066683268740.4254737929390.435228240309-33.91268681636.91373698174
233.41485173234-0.177431871160.07878870762562.07015158674-0.8110493178381.379637880530.238854362448-0.159746241545-0.101607562331-0.145206445721-0.0730188535472-0.01949663545270.04572353672930.1843168075410.129916504827-0.29019210885-0.04630743673370.2524955663190.38254049098-0.0424647877951-0.0371709595310.2113033725-27.347536817714.3271703232
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 27 through 89 )AA27 - 891 - 63
22chain 'A' and (resid 90 through 106 )AA90 - 10664 - 80
33chain 'A' and (resid 107 through 133 )AA107 - 13381 - 107
44chain 'A' and (resid 134 through 152 )AA134 - 152108 - 126
55chain 'A' and (resid 153 through 221 )AA153 - 221127 - 195
66chain 'B' and (resid 27 through 49 )BJ27 - 491 - 23
77chain 'B' and (resid 50 through 132 )BJ50 - 13224 - 106
88chain 'B' and (resid 133 through 165 )BJ133 - 165107 - 139
99chain 'B' and (resid 166 through 221 )BJ166 - 221140 - 195
1010chain 'E' and (resid 2 through 25 )ER2 - 251 - 24
1111chain 'E' and (resid 26 through 53 )ER26 - 5325 - 52
1212chain 'E' and (resid 54 through 92 )ER54 - 9253 - 91
1313chain 'E' and (resid 93 through 126 )ER93 - 12692 - 125
1414chain 'F' and (resid 2 through 17 )FT2 - 171 - 16
1515chain 'F' and (resid 18 through 61 )FT18 - 6117 - 58
1616chain 'F' and (resid 62 through 68 )FT62 - 6859 - 65
1717chain 'F' and (resid 69 through 126 )FT69 - 12666 - 123
1818chain 'D' and (resid 3 through 25 )DV3 - 251 - 23
1919chain 'D' and (resid 26 through 33 )DV26 - 3324 - 31
2020chain 'D' and (resid 34 through 126 )DV34 - 12632 - 124
2121chain 'C' and (resid 3 through 18 )CY3 - 181 - 16
2222chain 'C' and (resid 19 through 33 )CY19 - 3317 - 28
2323chain 'C' and (resid 34 through 126 )CY34 - 12629 - 121

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