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- PDB-8yaa: Cryo-EM structure of MIK2-SCOOP12-BAK1 -

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Basic information

Entry
Database: PDB / ID: 8yaa
TitleCryo-EM structure of MIK2-SCOOP12-BAK1
Components
  • BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
  • MDIS1-interacting receptor like kinase 2
  • Serine rich endogenous peptide 12
KeywordsTRANSFERASE/PLANT PROTEIN / LRR-RLK / SERK / MIK2 / SCOOP / BAK1 / PLANT PROTEIN / TRANSFERASE / PLANT PROTEIN complex / TRANSFERASE-PLANT PROTEIN complex
Function / homology
Function and homology information


plant-type cell wall organization / indole glucosinolate biosynthetic process / regulation of unidimensional cell growth / positive regulation of defense response / regulation of root development / regulation of defense response to fungus / pollen tube / cell-cell signaling involved in cell fate commitment / regulation of defense response to bacterium / pollen tube guidance ...plant-type cell wall organization / indole glucosinolate biosynthetic process / regulation of unidimensional cell growth / positive regulation of defense response / regulation of root development / regulation of defense response to fungus / pollen tube / cell-cell signaling involved in cell fate commitment / regulation of defense response to bacterium / pollen tube guidance / response to herbivore / regulation of root meristem growth / defense response to insect / response to insect / peptide receptor activity / LRR domain binding / jasmonic acid biosynthetic process / cellular response to peptide / apoplast / plasmodesma / receptor serine/threonine kinase binding / regulation of reactive oxygen species metabolic process / negative regulation of reactive oxygen species metabolic process / transmembrane receptor protein tyrosine kinase activity / response to bacterium / peptide binding / response to molecule of bacterial origin / receptor protein-tyrosine kinase / defense response / response to wounding / non-specific serine/threonine protein kinase / endosome membrane / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / identical protein 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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic 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
Serine rich endogenous peptide 12 / MDIS1-interacting receptor like kinase 2 / BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsJia, F.S. / Xiao, Y. / Chai, J.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat.Plants / Year: 2024
Title: N-glycosylation facilitates the activation of a plant cell-surface receptor
Authors: Jia, F. / Xiao, Y. / Feng, Y. / Yan, J. / Fan, M. / Sun, Y. / Huang, S. / Li, W. / Zhao, T. / Han, Z. / Hou, S. / Chai, J.
History
DepositionFeb 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
A: MDIS1-interacting receptor like kinase 2
B: Serine rich endogenous peptide 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,84923
Polymers92,3383
Non-polymers7,51120
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules CA

#1: Protein BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 / AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor ...AtBAK1 / BRI1-associated receptor kinase 1 / Protein ELONGATED / Somatic embryogenesis receptor kinase 3 / AtSERK3 / Somatic embryogenesis receptor-like kinase 3


Mass: 19160.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: BAK1, ELG, SERK3, At4g33430, F17M5.190 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q94F62, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase
#2: Protein MDIS1-interacting receptor like kinase 2 / AtMIK2 / Probable LRR receptor-like serine/threonine-protein kinase At4g08850


Mass: 71858.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MIK2, At4g08850, T32A17.160 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q8VZG8, non-specific serine/threonine protein kinase

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Protein/peptide , 1 types, 1 molecules B

#3: Protein/peptide Serine rich endogenous peptide 12 / AtSCOOP12 / Phytocytokine SCOOP12 / Precursor of serine rich endogenous peptide phytocytokine 12


Mass: 1318.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: B3H7I1

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Sugars , 4 types, 20 molecules

#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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_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]{}}}}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.: 10 / 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
#6: 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
#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.: 8 / 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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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of MIK2-SCOOP12-BAK1 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis (plant)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 6
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 319127 / Symmetry type: POINT
RefinementHighest resolution: 3.34 Å

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