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- PDB-8wef: Crystal structure of Brassica napus MIK2 ectodomain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8wef
TitleCrystal structure of Brassica napus MIK2 ectodomain in complex with Fusarium oxysporum SCOOPL
Components
  • MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2
  • a SCOOP-like peptide from F. oxysporum f. sp. conglutinans strain Fo5176
KeywordsPLANT PROTEIN / LRR receptor-like serine/threonine-protein kinase
Function / homology
Function and homology information


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
(rape) hypothetical protein
Similarity search - Component
Biological speciesBrassica napus (rape)
Fusarium oxysporum f. sp. pisi HDV247 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: MALE DISCOVERER 1-INTERACTING RECEPTOR-LIKE KINASE 2
C: a SCOOP-like peptide from F. oxysporum f. sp. conglutinans strain Fo5176
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,61011
Polymers75,5802
Non-polymers4,0309
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint57 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.959, 155.959, 125.087
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 / Protein/peptide / Non-polymers , 3 types, 172 molecules AC

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


Mass: 74230.602 Da / Num. of mol.: 1
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
#2: Protein/peptide a SCOOP-like peptide from F. oxysporum f. sp. conglutinans strain Fo5176


Mass: 1349.348 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Fusarium oxysporum f. sp. pisi HDV247 (fungus)
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 5 types, 9 molecules

#3: 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: obtained synthetically
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
#4: 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.: 4 / Source method: obtained synthetically
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
#5: 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: obtained synthetically
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
#6: 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: obtained synthetically
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
#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 / 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: 5.57 Å3/Da / Density % sol: 77.93 %
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: 2.8→50 Å / Num. obs: 43756 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.99 / Net I/σ(I): 12.2
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 4172 / CC1/2: 0.62

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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: 2.8→29.71 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 2178 5.04 %
Rwork0.1848 --
obs0.1862 43198 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5014 0 266 170 5450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.658
X-RAY DIFFRACTIONf_dihedral_angle_d9.109812
X-RAY DIFFRACTIONf_chiral_restr0.047908
X-RAY DIFFRACTIONf_plane_restr0.005925
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.2531500.24512474X-RAY DIFFRACTION96
2.86-2.920.30561220.22242494X-RAY DIFFRACTION97
2.92-30.27451420.22632488X-RAY DIFFRACTION97
3-3.080.2471240.22672538X-RAY DIFFRACTION98
3.08-3.170.2941240.23922555X-RAY DIFFRACTION99
3.17-3.270.28321250.24092560X-RAY DIFFRACTION99
3.27-3.390.26031580.23022568X-RAY DIFFRACTION100
3.39-3.520.2681140.20872549X-RAY DIFFRACTION100
3.52-3.680.23461670.18712559X-RAY DIFFRACTION100
3.68-3.870.20041110.17482607X-RAY DIFFRACTION100
3.87-4.120.19841540.15872564X-RAY DIFFRACTION100
4.12-4.430.15751410.14142608X-RAY DIFFRACTION100
4.43-4.880.14311370.14262599X-RAY DIFFRACTION100
4.88-5.580.1961340.16732606X-RAY DIFFRACTION99
5.58-7.010.21551640.18612595X-RAY DIFFRACTION99
7.02-29.710.20441110.19832656X-RAY DIFFRACTION96
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)
11.1796-0.56860.57921.8793-0.81831.535-0.0096-0.04840.09-0.10040.0529-0.016-0.13050.1236-0.01450.3864-0.02090.08280.4187-0.03240.353882.0762-40.085533.5256
23.00971.848-1.33984.5124-1.76312.9240.0553-0.083-0.3443-0.4519-0.3155-0.64750.35790.68330.26960.71090.14480.02430.55210.07170.509991.15674.48527.8377
32.1151.9491.17323.0036-1.39815.7402-0.6721-2.173-1.03220.78470.70070.0580.4138-1.4582-0.0431.38310.11620.13961.53860.27711.213885.0611-39.448840.3144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 425 )
2X-RAY DIFFRACTION2chain 'A' and (resid 426 through 674 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 5 )

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