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- PDB-9hhu: Plant membrane receptor IGP1 in complex with cellotriose -

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Basic information

Entry
Database: PDB / ID: 9hhu
TitlePlant membrane receptor IGP1 in complex with cellotriose
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
beta-cellotriose / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 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 in complex with cellotriose
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)72,54415
Polymers67,7271
Non-polymers4,81714
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Elution of the cellotriose complex has the profile of the monomeric IGP1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint26 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.775, 83.775, 198.935
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 , 6 types, 9 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-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_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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-ROHGlycam 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
[][D-1-deoxy-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
#5: 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
#6: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotriose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}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

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Non-polymers , 3 types, 193 molecules

#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 100 mM Sodium acetate pH 4.6, 200 mM Ammonium sulfate, 30 % w/v 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: Mar 27, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033286 Å / Relative weight: 1
ReflectionResolution: 2.16→48.95 Å / Num. obs: 42267 / % possible obs: 100 % / Redundancy: 7.8 % / Biso Wilson estimate: 45.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.069 / Rrim(I) all: 0.138 / Χ2: 0.93 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.91-48.957.80.03635.16300.9990.020.0410.8999.1
2.16-2.236.52.067136330.3161.3362.4740.93100

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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: 2.16→48.95 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 11.707 / SU ML: 0.146 / Cross valid method: FREE R-VALUE / ESU R: 0.183 / ESU R Free: 0.163
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2105 2076 4.92 %
Rwork0.169 40118 -
all0.171 --
obs-42194 99.983 %
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: 51.647 Å2
Baniso -1Baniso -2Baniso -3
1-0.537 Å20.269 Å2-0 Å2
2--0.537 Å2-0 Å2
3----1.743 Å2
Refinement stepCycle: LAST / Resolution: 2.16→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 312 188 4948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0124883
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164400
X-RAY DIFFRACTIONr_angle_refined_deg2.2891.8086699
X-RAY DIFFRACTIONr_angle_other_deg0.7741.72510204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.635609
X-RAY DIFFRACTIONr_dihedral_angle_other_1_deg4.4392014
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.887520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16210.139717
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.67710184
X-RAY DIFFRACTIONr_chiral_restr0.1040.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025556
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021064
X-RAY DIFFRACTIONr_nbd_refined0.2180.2930
X-RAY DIFFRACTIONr_symmetry_nbd_other0.210.24275
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22554
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.22695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1410.28
X-RAY DIFFRACTIONr_nbd_other0.2310.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0810.23
X-RAY DIFFRACTIONr_mcbond_it3.8073.1252376
X-RAY DIFFRACTIONr_mcbond_other3.8063.1252376
X-RAY DIFFRACTIONr_mcangle_it5.355.6052970
X-RAY DIFFRACTIONr_mcangle_other5.3495.6072971
X-RAY DIFFRACTIONr_scbond_it6.1523.9972507
X-RAY DIFFRACTIONr_scbond_other6.1123.9752492
X-RAY DIFFRACTIONr_scangle_it8.3187.2043729
X-RAY DIFFRACTIONr_scangle_other8.287.1673706
X-RAY DIFFRACTIONr_lrange_it8.62631.6435306
X-RAY DIFFRACTIONr_lrange_other8.62931.4765291
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.16-2.2160.3421700.30429240.30630940.910.931000.307
2.216-2.2770.2711770.27528510.27530280.9470.9451000.277
2.277-2.3430.2621720.2427890.24229610.9570.9611000.241
2.343-2.4140.3011290.23627370.23928660.940.9651000.233
2.414-2.4930.2511410.22126170.22327590.9590.97399.96380.215
2.493-2.5810.2521090.19125790.19426880.9610.981000.181
2.581-2.6780.2531040.18224890.18525930.9650.9821000.169
2.678-2.7870.2451300.15723940.16225240.9660.9871000.144
2.787-2.910.2281070.15322780.15623850.9710.9871000.137
2.91-3.0520.2051100.15321620.15622720.9720.9861000.139
3.052-3.2160.178930.14221090.14322020.9780.9881000.131
3.216-3.410.21940.16719500.16920440.9680.9851000.158
3.41-3.6450.208880.17118730.17319610.9730.9861000.166
3.645-3.9350.208840.15417050.15617890.9780.9891000.152
3.935-4.3080.143710.12315930.12416640.9890.9941000.125
4.308-4.8110.138860.10914290.1115150.990.9931000.113
4.811-5.5470.172780.13312630.13513410.9810.9911000.138
5.547-6.7720.262550.19110630.19511180.9640.9841000.198
6.772-9.4870.237460.2178400.2188860.9750.981000.226
9.487-48.950.217320.2164730.2165080.9710.97299.40940.233
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)
11.40920.2416-0.30521.7184-1.16252.60430.02470.0651-0.1705-0.18180.0111-0.11580.24030.0335-0.03570.0772-0.01020.05710.0105-0.02030.156126.92-20.119-22.714
21.4683-0.2973-0.19691.6259-0.07362.4146-0.1062-0.2466-0.06720.177-0.035-0.2799-0.08150.50590.14120.0607-0.0148-0.0340.18960.13930.221636.288-25.8515.401
33.8336-1.9553-0.7499.2070.69478.90390.14630.39740.51810.0188-0.06960.1-0.1532-0.3168-0.07670.2336-0.0612-0.08750.10120.07660.165820.273-8.5228.259
41.1524-0.0255-1.01492.068-1.39586.2372-0.0616-0.077-0.06880.06830.0850.1814-0.1037-0.3562-0.02340.0468-0.01170.00060.08210.04670.202617.798-21.59111.671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp28 - 285
2X-RAY DIFFRACTION2ALLAp286 - 467
3X-RAY DIFFRACTION3ALLAp468 - 495
4X-RAY DIFFRACTION4ALLAp496 - 622

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