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- PDB-8wei: Crystal structure of Brassica napus MIK2 ectodomain (N393D mutant) -

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Basic information

Entry
Database: PDB / ID: 8wei
TitleCrystal structure of Brassica napus MIK2 ectodomain (N393D mutant)
ComponentsMALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2
KeywordsPLANT PROTEIN / LRR receptor-like serine/threonine-protein kinase
Function / homology
Function and homology information


non-specific serine/threonine protein kinase / protein 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 region / 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-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / : / Leucine-rich repeat region / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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
non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesBrassica napus (rape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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

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Assembly

Deposited unit
A: MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,32510
Polymers77,4981
Non-polymers3,8279
Water3,819212
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)155.895, 155.895, 126.651
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Non-polymers , 2 types, 213 molecules A

#1: Protein MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2


Mass: 77498.469 Da / Num. of mol.: 1 / Mutation: N393D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Gene: DARMORV10_C03P34170.1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A816I5A6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 9 molecules

#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.: 3
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: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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.: 1
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
#5: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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.: 3 / 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

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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: 5.73 Å3/Da / Density % sol: 78.54 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 8.5
Details: 0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 34% w/v PEG 400

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 49088 / % possible obs: 100 % / Redundancy: 5.8 % / CC1/2: 0.98 / Net I/σ(I): 10.7
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 1468 / CC1/2: 0.57

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→36.68 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2162 2211 4.99 %
Rwork0.1994 --
obs0.2002 44279 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→36.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 0 252 212 5445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.66
X-RAY DIFFRACTIONf_dihedral_angle_d8.006802
X-RAY DIFFRACTIONf_chiral_restr0.046898
X-RAY DIFFRACTIONf_plane_restr0.004919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.770.4091110.355306X-RAY DIFFRACTION11
2.77-2.830.3662740.30791863X-RAY DIFFRACTION64
2.83-2.90.2881510.2652516X-RAY DIFFRACTION90
2.9-2.980.31441450.26182775X-RAY DIFFRACTION97
2.98-3.070.30351250.26052877X-RAY DIFFRACTION99
3.07-3.170.27251580.24922845X-RAY DIFFRACTION100
3.17-3.280.28371800.2332818X-RAY DIFFRACTION100
3.28-3.410.22441570.2292849X-RAY DIFFRACTION100
3.41-3.570.21741340.2052877X-RAY DIFFRACTION100
3.57-3.750.18921260.17722884X-RAY DIFFRACTION100
3.75-3.990.19351580.17112887X-RAY DIFFRACTION100
3.99-4.30.15041570.1482873X-RAY DIFFRACTION100
4.3-4.730.15581480.14862911X-RAY DIFFRACTION100
4.73-5.410.18311440.17312904X-RAY DIFFRACTION99
5.41-6.810.21061520.21072912X-RAY DIFFRACTION99
6.81-36.680.22931910.20562971X-RAY DIFFRACTION98
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)
10.9784-0.4847-0.48491.56040.87411.7587-0.0158-0.0425-0.0872-0.0560.05580.08220.119-0.1151-0.02860.1954-0.0287-0.06060.20940.0410.1857-81.82639.361233.5893
22.55311.48531.27533.25341.40072.6022-0.076-0.08750.3781-0.3567-0.1950.58-0.4375-0.58540.20110.57130.1372-0.02630.3602-0.05080.4137-91.885-4.74397.6356
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 432 )
2X-RAY DIFFRACTION2chain 'A' and (resid 433 through 674 )

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