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- PDB-9hhx: Plant membrane receptor IGP1 -

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Basic information

Entry
Database: PDB / ID: 9hhx
TitlePlant membrane receptor IGP1
Componentsnon-specific serine/threonine protein kinase
KeywordsPLANT PROTEIN / Receptor / cellotriose binding protein / signal transduction / plant immunity
Function / homology
Function and homology information


plasmodesma / kinase activity / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane
Similarity search - Function
Malectin domain / Malectin domain / : / Leucine Rich Repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Malectin domain / Malectin domain / : / Leucine Rich Repeat / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / 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 speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsJimenez-Sandoval, P. / Santiago, J.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030_200528 Switzerland
European Research Council (ERC)716358European Union
CitationJournal: To Be Published
Title: Plant membrane receptor IGP1
Authors: Jimenez-Sandoval, P. / Santiago, J.
History
DepositionNov 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,83714
Polymers67,7271
Non-polymers4,11013
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Elution has the profile of the monomeric IGP1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint16 kcal/mol
Surface area25530 Å2
Unit cell
Length a, b, c (Å)84.365, 84.365, 198.32
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein non-specific serine/threonine protein kinase


Mass: 67726.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: LRR-RLK, At1g56145 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: C0LGH4, non-specific serine/threonine protein kinase

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Sugars , 4 types, 8 molecules

#2: 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.: 2
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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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.: 4 / 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

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Non-polymers , 3 types, 60 molecules

#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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 Å3/Da / Density % sol: 59.17 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M Sodium acetate trihydrate pH 4.6 0.2 M Ammonium sulfate 30 % PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.033286 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033286 Å / Relative weight: 1
ReflectionResolution: 2.62→49.58 Å / Num. obs: 24021 / % possible obs: 100 % / Redundancy: 10.5 % / CC1/2: 0.973 / Rmerge(I) obs: 0.428 / Rpim(I) all: 0.205 / Rrim(I) all: 0.475 / Χ2: 1.01 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
9.08-49.5810.60.0727.16010.9980.0330.0780.9199.5
2.62-2.748.72.114129350.3141.1472.4120.98100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
pointless1.13.4data scaling
Aimless0.8.2data scaling
Coot0.9.8.95model building
PHENIX2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→49.068 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.883 / SU B: 29.983 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / ESU R: 0.565 / ESU R Free: 0.314
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2564 1185 4.945 %
Rwork0.1823 22777 -
all0.186 --
obs-23962 99.987 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.261 Å2
Baniso -1Baniso -2Baniso -3
1-0.442 Å20.221 Å20 Å2
2--0.442 Å2-0 Å2
3----1.434 Å2
Refinement stepCycle: LAST / Resolution: 2.62→49.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4479 0 264 55 4798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124863
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164473
X-RAY DIFFRACTIONr_angle_refined_deg2.3351.8276662
X-RAY DIFFRACTIONr_angle_other_deg0.7881.75610319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7485594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.944523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30910722
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.12410190
X-RAY DIFFRACTIONr_chiral_restr0.1020.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025600
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021096
X-RAY DIFFRACTIONr_nbd_refined0.2150.2924
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.24321
X-RAY DIFFRACTIONr_nbtor_refined0.1880.22500
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0950.22705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2121
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1210.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.215
X-RAY DIFFRACTIONr_nbd_other0.2180.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.25
X-RAY DIFFRACTIONr_mcbond_it2.5212.4992376
X-RAY DIFFRACTIONr_mcbond_other2.5172.52376
X-RAY DIFFRACTIONr_mcangle_it44.4912970
X-RAY DIFFRACTIONr_mcangle_other44.4922971
X-RAY DIFFRACTIONr_scbond_it3.9743.0642487
X-RAY DIFFRACTIONr_scbond_other3.8243.0432472
X-RAY DIFFRACTIONr_scangle_it5.9735.5493692
X-RAY DIFFRACTIONr_scangle_other5.8385.5153669
X-RAY DIFFRACTIONr_lrange_it6.80425.8485173
X-RAY DIFFRACTIONr_lrange_other6.81725.8575174
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
2.62-2.6880.3331040.32616620.32717660.8990.9220.329
2.688-2.7610.358840.30316390.30617230.9140.9350.305
2.761-2.8410.3391110.28315550.28716660.9240.9480.285
2.841-2.9280.357710.26615680.26916390.9210.9540.263
2.928-3.0240.297870.24114810.24415680.9390.9650.235
3.024-3.130.288840.21414480.21815320.9430.9710.205
3.13-3.2470.249660.19114110.19414770.960.9760.177
3.247-3.3790.287650.18613500.1914150.9460.9780.171
3.379-3.5290.263610.18512890.18913500.9460.9790.169
3.529-3.70.238550.16512350.16812900.9650.9850.15
3.7-3.8990.239650.15511570.1612220.9710.9870.139
3.899-4.1340.197630.13511210.13911840.9780.990.119
4.134-4.4170.192470.11410530.11711000.980.9930.099
4.417-4.7680.198650.1159560.1210210.9790.9930.096
4.768-5.2180.195440.1259050.1299490.9780.9910.109
5.218-5.8260.199290.1428230.1448520.9810.9890.122
5.826-6.7110.275310.1637290.1677600.9630.9850.139
6.711-8.1810.231250.1726190.1746440.9660.9840.152
8.181-11.4120.299140.1574930.165070.9550.9850.14
11.412-49.0680.295140.2092830.2122970.9270.9710.2
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)
11.2594-0.14270.56110.58090.0341.36740.0325-0.10540.08390.01850.0315-0.0228-0.0363-0.1478-0.0640.02870.00460.00120.03590.00350.0162-3.933333.432822.8388
20.90620.0709-0.12290.7237-0.05631.2523-0.00040.01720.1002-0.1161-0.0092-0.113-0.19540.14750.00960.1015-0.01860.00420.07860.0260.0426-4.238144.5877-14.8386
33.1319-1.18681.46071.85660.06525.5198-0.0243-0.0289-0.30820.17350.031-0.03760.1540.3069-0.00670.0357-0.0149-0.0070.0610.00750.0577-3.078924.6272-12.4295
40.7894-0.29040.87990.74610.14264.2760.0977-0.0074-0.1319-0.0929-0.05310.01920.2644-0.0132-0.04460.0432-0.0225-0.01280.07030.02360.0618-10.503826.0042-10.4962
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp30 - 284
2X-RAY DIFFRACTION2ALLAp285 - 470
3X-RAY DIFFRACTION3ALLAp471 - 527
4X-RAY DIFFRACTION4ALLAp528 - 622

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