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- PDB-8web: Crystal structure of Arabidopsis thaliana MIK2 ectodomain -

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Basic information

Entry
Database: PDB / ID: 8web
TitleCrystal structure of Arabidopsis thaliana MIK2 ectodomain
ComponentsMDIS1-interacting receptor like kinase 2
KeywordsPLANT PROTEIN / LRR receptor-like serine/threonine-protein kinase
Function / homology
Function and homology information


indole glucosinolate biosynthetic process / positive regulation of defense response / pollen tube / pollen tube guidance / response to herbivore / defense response to insect / peptide receptor activity / jasmonic acid biosynthetic process / cellular response to peptide / plasmodesma ...indole glucosinolate biosynthetic process / positive regulation of defense response / pollen tube / pollen tube guidance / response to herbivore / defense response to insect / peptide receptor activity / jasmonic acid biosynthetic process / cellular response to peptide / plasmodesma / peptide binding / response to molecule of bacterial origin / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein serine kinase activity / ATP binding / plasma membrane
Similarity search - Function
: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein kinase 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
MDIS1-interacting receptor like kinase 2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWan, L.H. / Hu, Y.X. / Wu, H.M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000900 China
CitationJournal: Nat.Plants / Year: 2024
Title: Mechanistic study of SCOOPs recognition by MIK2-BAK1 complex reveals the role of N-glycans in plant ligand-receptor-coreceptor complex formation.
Authors: Wu, H. / Wan, L. / Liu, Z. / Jian, Y. / Zhang, C. / Mao, X. / Wang, Z. / Wang, Q. / Hu, Y. / Xiong, L. / Xia, Z. / Xue, J. / Li, S. / He, P. / Shan, L. / Xu, S.
History
DepositionSep 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 25, 2024Group: 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: MDIS1-interacting receptor like kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,50612
Polymers78,8541
Non-polymers3,65211
Water11,926662
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.127, 107.889, 164.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MDIS1-interacting receptor like kinase 2 / AtMIK2 / Probable LRR receptor-like serine/threonine-protein kinase At4g08850


Mass: 78853.930 Da / Num. of mol.: 1 / Mutation: L137E/D164K/S564F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MIK2, At4g08850, T32A17.160 / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q8VZG8, non-specific serine/threonine protein kinase
#2: 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.: 6
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
#3: 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: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O
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: 3.49 Å3/Da / Density % sol: 64.77 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7.4
Details: 0.2 M Sodium acetate, 0.1 M Tris pH 7.4 and 18% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 81379 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 1 / Net I/σ(I): 32.9
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 6952 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.20.1_4487: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→35.13 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 3954 4.94 %
Rwork0.171 --
obs0.1725 80038 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5009 0 238 662 5909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017
X-RAY DIFFRACTIONf_angle_d1.268
X-RAY DIFFRACTIONf_dihedral_angle_d19.132006
X-RAY DIFFRACTIONf_chiral_restr0.091887
X-RAY DIFFRACTIONf_plane_restr0.012930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.3002910.26671876X-RAY DIFFRACTION69
1.97-20.25821400.23542564X-RAY DIFFRACTION94
2-2.020.24511310.21562669X-RAY DIFFRACTION99
2.02-2.050.2671430.2012711X-RAY DIFFRACTION99
2.05-2.080.22551480.19892729X-RAY DIFFRACTION100
2.08-2.110.19431310.18222739X-RAY DIFFRACTION100
2.11-2.150.23081490.17512693X-RAY DIFFRACTION100
2.15-2.180.22641400.17932698X-RAY DIFFRACTION100
2.18-2.220.21411470.18932752X-RAY DIFFRACTION100
2.22-2.260.24411410.17592728X-RAY DIFFRACTION100
2.26-2.30.23621380.18022723X-RAY DIFFRACTION100
2.3-2.350.23371370.17362733X-RAY DIFFRACTION100
2.35-2.40.21871310.15732761X-RAY DIFFRACTION100
2.4-2.460.19091500.15482722X-RAY DIFFRACTION100
2.46-2.520.17981670.1562694X-RAY DIFFRACTION100
2.52-2.590.18081350.15422777X-RAY DIFFRACTION100
2.59-2.660.18781350.15462730X-RAY DIFFRACTION100
2.66-2.750.20121470.16012745X-RAY DIFFRACTION100
2.75-2.850.20021350.16582769X-RAY DIFFRACTION100
2.85-2.960.21511310.1722770X-RAY DIFFRACTION100
2.96-3.090.19071400.18562756X-RAY DIFFRACTION100
3.09-3.260.25731570.1852761X-RAY DIFFRACTION100
3.26-3.460.2291570.18672769X-RAY DIFFRACTION100
3.46-3.730.1891440.16892770X-RAY DIFFRACTION100
3.73-4.10.15091550.14532793X-RAY DIFFRACTION100
4.1-4.70.15941410.12222823X-RAY DIFFRACTION100
4.7-5.910.17031460.16122856X-RAY DIFFRACTION100
5.91-35.130.19041470.20252973X-RAY DIFFRACTION99
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)
11.08671.0719-0.21742.9077-1.0781.70230.1387-0.0383-0.04730.0488-0.05820.11810.0185-0.0059-0.07410.17880.02020.00340.1345-0.03240.096723.0156-23.969226.714
20.46560.3253-0.28260.8501-0.87652.23760.0499-0.04110.00030.1283-0.0843-0.0404-0.02040.26460.03060.11830.01280.03530.16150.00290.141438.88890.8-1.691
33.4612-0.90981.57851.7415-0.31211.41590.05480.1546-0.1959-0.17640.00970.02090.1730.1041-0.05820.1394-0.02110.03880.14660.00940.141822.89613.8566-26.6643
43.4019-0.3266-1.23922.0161-0.13411.7080.1519-0.12420.21060.00510.00910.2958-0.1742-0.0921-0.13450.1236-0.0524-0.02090.1670.03030.159-3.187118.6817-24.4633
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 47 through 244 )
2X-RAY DIFFRACTION2chain 'A' and (resid 245 through 427 )
3X-RAY DIFFRACTION3chain 'A' and (resid 428 through 512 )
4X-RAY DIFFRACTION4chain 'A' and (resid 513 through 696 )

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