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- PDB-8ps7: Crystal structure of Medicago truncatula LYR4 kinase domain -

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Basic information

Entry
Database: PDB / ID: 8ps7
TitleCrystal structure of Medicago truncatula LYR4 kinase domain
ComponentsLysM-domain receptor-like kinase
KeywordsPLANT PROTEIN / Kinase / Immunity / LysM
Function / homology
Function and homology information


protein kinase activity / ATP binding / membrane
Similarity search - Function
: / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Protein kinase domain / 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
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSimonsen, B. / Gysel, K. / Laursen, M. / Andersen, K.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0052855 Denmark
Citation
Journal: New Phytol. / Year: 2025
Title: The Medicago truncatula LYR4 intracellular domain serves as a scaffold in immunity signaling independent of its phosphorylation activity.
Authors: Simonsen, B. / Rubsam, H. / Kolte, M.V. / Larsen, M.M. / Kronauer, C. / Gysel, K. / Laursen, M. / Feng, F. / Kaya, G. / Oldroyd, G.E.D. / Stougaard, J. / Fort, S. / Radutoiu, S. / Andersen, K.R.
#1: Journal: Biorxiv / Year: 2024
Title: The Medicago truncatula LYR4 intracellular domain serves as a scaffold in immunity signaling independent of its phosphorylation activity
Authors: Simonsen, B. / Rubsam, H. / Kolte, M.V. / Larsen, M.M. / Kronauer, C. / Gysel, K. / Laursen, M. / Feng, F. / Kaya, G. / Oldroyd, G.E.D. / Stougaard, J. / Fort, S. / Radutoiu, S. / Andersen, K.R.
History
DepositionJul 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Revision 1.2May 7, 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
B: LysM-domain receptor-like kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3409
Polymers66,8602
Non-polymers1,4817
Water3,117173
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A: LysM-domain receptor-like kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2165
Polymers33,4301
Non-polymers7864
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LysM-domain receptor-like kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1244
Polymers33,4301
Non-polymers6943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.684, 78.242, 70.365
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein LysM-domain receptor-like kinase


Mass: 33429.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11433363, MTR_5g085790, MtrunA17_Chr5g0439331 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: G7K7K0
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.13 Å3/Da / Density % sol: 42.19 % / Description: Needles
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ammonium sulfate, sodium cacodylate trihydrate, PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979491 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979491 Å / Relative weight: 1
ReflectionResolution: 2.1→43.124 Å / Num. obs: 18580 / % possible obs: 91.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.79 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.24 / Net I/σ(I): 5.2
Reflection shellResolution: 2.1→2.34 Å / Num. unique obs: 929 / CC1/2: 0.62 / % possible all: 70.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.12 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.557
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.269 1465 7.89 %
Rwork0.221 --
obs0.225 18578 56.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.61 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 90 173 4646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024552
X-RAY DIFFRACTIONf_angle_d0.4796151
X-RAY DIFFRACTIONf_dihedral_angle_d13.5161670
X-RAY DIFFRACTIONf_chiral_restr0.038676
X-RAY DIFFRACTIONf_plane_restr0.002785
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.3576130.315191X-RAY DIFFRACTION3
2.18-2.260.3212420.2941356X-RAY DIFFRACTION12
2.26-2.370.3218560.3142568X-RAY DIFFRACTION19
2.37-2.490.357650.2882854X-RAY DIFFRACTION28
2.49-2.650.32281020.28121318X-RAY DIFFRACTION44
2.65-2.850.27211830.27392101X-RAY DIFFRACTION70
2.85-3.140.30582640.25092672X-RAY DIFFRACTION90
3.14-3.590.27742500.21153012X-RAY DIFFRACTION100
3.59-4.530.22112440.17973030X-RAY DIFFRACTION100
4.53-43.120.26222460.20993111X-RAY DIFFRACTION100
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)
12.80662.4763-1.97584.7848-0.09662.4826-0.14150.44090.3165-0.4185-0.1611-0.39570.0967-0.09070.26780.374-0.0071-0.00480.46360.01630.4212-32.63849.2838-2.0069
29.46650.1268-3.08366.0648-4.68224.55630.5339-1.66871.06991.0767-0.605-0.7704-1.21561.1638-0.06210.4998-0.2810.10210.7107-0.01760.3401-20.947416.31883.0988
32.943-0.6987-2.05182.2050.77492.86790.38610.06690.1927-0.0479-0.55410.1993-0.0392-0.67910.09930.2774-0.0078-0.02390.4238-0.01980.0943-21.02637.45-7.1383
41.5423-0.0703-0.19283.96840.01191.62620.01560.0574-0.0099-0.19590.04680.1464-0.35210.1026-0.05180.14440.00320.00090.20010.02170.0678-10.68716.1534-13.6389
52.968-2.36641.88641.9025-1.25843.63830.5954-0.2151-0.3897-0.3588-0.25640.23430.2108-0.5081-0.31690.3892-0.12790.01390.26860.02750.2545-9.52-0.4573.4941
60.8848-0.16030.54020.1099-0.24212.8216-0.005-0.0053-0.2258-0.08540.00140.04010.34460.3698-0.00880.20840.03440.04570.28670.04710.04070.0905-5.3119-4.8706
75.3434-0.5629-1.07081.1021-0.64234.2878-0.31080.63-0.8789-0.0820.13440.14620.3486-0.11170.13180.37440.0860.01230.2594-0.07090.169-1.2275-15.8376-19.9276
81.0023-0.0062-1.18563.61261.04434.04160.05170.26660.054-0.01020.0335-0.4571-0.16560.581-0.11590.10730.01480.06770.41430.04960.09322.52810.8646-17.5508
93.38910.46531.52332.19980.8931.90270.14270.0999-0.2548-0.5028-0.25990.47820.0643-0.42230.12430.32450.0002-0.03640.4571-0.02770.2465-21.466625.8865-31.4627
100.7227-0.8208-0.49461.6558-0.06650.7973-0.01630.0749-0.0914-0.12480.02730.22680.1520.1445-0.01940.1982-0.0265-0.01060.28230.01640.1173-4.93530.15-30.0186
111.7675-0.01030.37232.86760.19723.7137-0.11320.00960.2825-0.18540.1118-0.1165-0.31980.078-0.00960.14280.0005-0.00940.2005-0.00720.05313.911941.2277-20.2973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 340 THROUGH 375 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 376 THROUGH 391 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 392 THROUGH 446 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 447 THROUGH 492 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 493 THROUGH 522 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 523 THROUGH 577 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 578 THROUGH 599 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 600 THROUGH 636 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 340 THROUGH 446 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 447 THROUGH 534 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 535 THROUGH 636 )

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