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- PDB-9gfz: Crystal structure of Medicago Truncatula LYK3 kinase domain D459N -

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Basic information

Entry
Database: PDB / ID: 9gfz
TitleCrystal structure of Medicago Truncatula LYK3 kinase domain D459N
ComponentsLysM domain receptor-like kinase 3
KeywordsPLANT PROTEIN / Receptor kinase / root nodule symbiosis / RLK/Pelle
Function / homology
Function and homology information


transmembrane receptor protein kinase activity / nodulation / response to symbiotic bacterium / vacuolar lumen / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity ...transmembrane receptor protein kinase activity / nodulation / response to symbiotic bacterium / vacuolar lumen / kinase activity / protein autophosphorylation / non-specific serine/threonine protein kinase / innate immune response / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / LYK3/4/5 LysM2 domain / 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 ...: / LYK3/4/5 LysM2 domain / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / LysM domain receptor-like kinase 3
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSimonsen, B. / Gysel, K. / Andersen, C.G. / Andersen, K.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0052855 Denmark
Citation
Journal: Nature / Year: 2025
Title: Two residues reprogram immunity receptors for nitrogen-fixing symbiosis.
Authors: Tsitsikli, M. / Simonsen, B. / Luu, T.B. / Larsen, M.M. / Andersen, C.G. / Gysel, K. / Lironi, D. / Kronauer, C. / Rubsam, H. / Hansen, S.B. / Baerentsen, R. / Wulff, J.L. / Johansen, S.H. / ...Authors: Tsitsikli, M. / Simonsen, B. / Luu, T.B. / Larsen, M.M. / Andersen, C.G. / Gysel, K. / Lironi, D. / Kronauer, C. / Rubsam, H. / Hansen, S.B. / Baerentsen, R. / Wulff, J.L. / Johansen, S.H. / Sezer, G. / Stougaard, J. / Andersen, K.R. / Radutoiu, S.
#1: Journal: Biorxiv / Year: 2024
Title: Two residues reprogram immunity receptor kinases to signal in nitrogen-fixing symbiosis
Authors: Tsitsikli, M. / Simonsen, B.W. / Larsen, M.M. / Andersen, C.G. / Gysel, K. / Lironi, D. / Kronauer, C. / Rubsam, H. / Luu, T.B. / Hansen, S.B. / Kaya, G. / Stougaard, J. / Andersen, K.R. / Radutoiu, S.
History
DepositionAug 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Structure summary / Category: audit_author
Revision 1.2Dec 10, 2025Group: Database references / Category: citation / citation_author
Revision 1.3Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysM domain receptor-like kinase 3
B: LysM domain receptor-like kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4943
Polymers65,9882
Non-polymers5061
Water81145
1
A: LysM domain receptor-like kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5002
Polymers32,9941
Non-polymers5061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LysM domain receptor-like kinase 3


Theoretical massNumber of molelcules
Total (without water)32,9941
Polymers32,9941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.980, 59.840, 61.240
Angle α, β, γ (deg.)99.905, 105.750, 119.799
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein LysM domain receptor-like kinase 3 / LysM-containing receptor-like kinase 3 / MtLYK3 / LysM receptor kinase K1B / Protein HAIR CURLING


Mass: 32994.051 Da / Num. of mol.: 2 / Mutation: D459N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: LYK3, HCL, RLK3, MTR_5g086130 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6UD73, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium Formate, 0.1 M Bis-Tris propane pH 8.5, 20% w/v PEG 3350, 6 mM AMP-PNP

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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: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.5→42.99 Å / Num. obs: 20193 / % possible obs: 99.76 % / Redundancy: 6.9 % / Biso Wilson estimate: 58.72 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.46
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.11 / Num. unique obs: 1443 / CC1/2: 0.683 / % possible all: 99.24

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→42.99 Å / SU ML: 0.3681 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.4186
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2568 1996 9.9 %
Rwork0.2062 18162 -
obs0.2111 20158 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.79 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4467 0 31 45 4543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00154584
X-RAY DIFFRACTIONf_angle_d0.42036206
X-RAY DIFFRACTIONf_chiral_restr0.0393709
X-RAY DIFFRACTIONf_plane_restr0.0029783
X-RAY DIFFRACTIONf_dihedral_angle_d11.62231720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.36621420.35271295X-RAY DIFFRACTION99.1
2.56-2.630.34671410.31851281X-RAY DIFFRACTION99.86
2.63-2.710.33081450.2821312X-RAY DIFFRACTION99.39
2.71-2.80.36961440.2621305X-RAY DIFFRACTION99.79
2.8-2.90.31781420.2721289X-RAY DIFFRACTION100
2.9-3.010.32171410.27311288X-RAY DIFFRACTION99.79
3.01-3.150.30091450.24571325X-RAY DIFFRACTION99.66
3.15-3.320.29261420.23861288X-RAY DIFFRACTION99.65
3.32-3.520.30421420.2181288X-RAY DIFFRACTION99.86
3.52-3.790.2761420.19291290X-RAY DIFFRACTION99.93
3.8-4.180.21771420.16931298X-RAY DIFFRACTION100
4.18-4.780.2071440.16611313X-RAY DIFFRACTION100
4.78-6.020.23031420.19741290X-RAY DIFFRACTION100
6.02-42.990.21531420.17611300X-RAY DIFFRACTION99.52
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)
18.52267995972-0.5895362145995.262149542167.525995443354.02658929257.50461734430.1910228258661.22664219224-0.00501287253244-1.149888392120.2594478792330.4661525416130.8439360365430.459593709663-0.4538156320831.06011228897-0.2576995943260.01465195703910.7851593733310.1468166568690.6370691324937.32418458368-24.306381332-25.9488165859
24.37071982214-0.608736486491-0.4315529971364.81516680313-1.191652540825.127738619720.0564825639885-0.06264947680110.164363079360.02662969786980.07438300736690.251063050539-0.204574385311-0.119076820169-0.1106480135250.453468431183-0.06620812201670.02191799262360.3683626487-0.01076039056580.25622868903615.3739747538-0.330198419987-18.2986834154
35.228417509943.332426062933.102266515324.77386492092-1.130776835975.76188063848-0.002721870261630.287021124103-1.26594212663-0.7368091973740.364870538063-0.2960703262821.36035549477-0.292397075748-0.4220843460161.198427208430.024734374280.2396293895050.849699973915-0.2096903670570.77614201190617.5150988846-37.438872268-0.00169333292423
46.395022810830.2084125511010.7572365425994.06725474463-1.808445634486.09522746361-0.0455168933114-0.143741111499-0.0738329179066-0.030290901411-0.21106843337-0.3276494660820.0106210356770.7365409996150.1794773697390.463256703633-0.001230089750160.03111368991380.4777381415450.05037500300650.31763461772223.2017878106-18.126697546312.2429329759
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 302 through 391 )AA302 - 3911 - 90
22chain 'A' and (resid 392 through 596 )AA392 - 59691 - 288
33chain 'B' and (resid 307 through 411 )BC307 - 4111 - 105
44chain 'B' and (resid 412 through 596 )BC412 - 596106 - 281

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