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- EMDB-39093: Cryo-EM structure of MIK2-SCOOP12-BAK1 -

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Basic information

Entry
Database: EMDB / ID: EMD-39093
TitleCryo-EM structure of MIK2-SCOOP12-BAK1
Map data
Sample
  • Complex: Ternary complex of MIK2-SCOOP12-BAK1
    • Protein or peptide: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
    • Protein or peptide: MDIS1-interacting receptor like kinase 2
    • Protein or peptide: Serine rich endogenous peptide 12
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLRR-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 / regulation of root development / positive regulation of defense response / pollen tube / cell-cell signaling involved in cell fate commitment / regulation of defense response to fungus / regulation of defense response to bacterium / pollen tube guidance ...plant-type cell wall organization / indole glucosinolate biosynthetic process / regulation of unidimensional cell growth / regulation of root development / positive regulation of defense response / pollen tube / cell-cell signaling involved in cell fate commitment / regulation of defense response to fungus / regulation of defense response to bacterium / pollen tube guidance / response to herbivore / regulation of root meristem growth / defense response to insect / response to insect / LRR domain binding / peptide receptor activity / 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 / peptide binding / response to bacterium / response to molecule of bacterial origin / defense response / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / response to wounding / 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 / endosome membrane / signaling receptor binding / protein serine 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 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-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 / 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 (plant) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsJia FS / Xiao Y / Chai JJ
Funding support China, 1 items
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: Fangshuai Jia / Yu Xiao / Yaojie Feng / Jinghui Yan / Mingzhu Fan / Yue Sun / Shijia Huang / Weiguo Li / Tian Zhao / Zhifu Han / Shuguo Hou / Jijie Chai /
Abstract: Plant receptor kinases (RKs) are critical for transmembrane signalling involved in various biological processes including plant immunity. MALE DISCOVERER1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) is ...Plant receptor kinases (RKs) are critical for transmembrane signalling involved in various biological processes including plant immunity. MALE DISCOVERER1-INTERACTING RECEPTOR-LIKE KINASE 2 (MIK2) is a unique RK that recognizes a family of immunomodulatory peptides called SERINE-RICH ENDOGENOUS PEPTIDEs (SCOOPs) and activates pattern-triggered immunity responses. However, the precise mechanisms underlying SCOOP recognition and activation of MIK2 remain poorly understood. Here we present the cryogenic electron microscopy structure of a ternary complex consisting of the extracellular leucine-rich repeat (LRR) of MIK2 (MIK2LRR), SCOOP12 and the extracellular LRR of the co-receptor BAK1 (BAK1LRR) at a resolution of 3.34 Å. The structure reveals that a DNHH motif in MIK2LRR plays a critical role in specifically recognizing the highly conserved SxS motif of SCOOP12. Furthermore, the structure demonstrates that N-glycans at MIK2LRR directly interact with the N-terminal capping region of BAK1LRR. Mutation of the glycosylation site, MIK2LRR, completely abolishes the SCOOP12-independent interaction between MIK2LRR and BAK1LRR and substantially impairs the assembly of the MIK2LRR-SCOOP12-BAK1LRR complex. Supporting the biological relevance of N410-glycosylation, MIK2 substantially compromises SCOOP12-triggered immune responses in plants. Collectively, these findings elucidate the mechanism underlying the loose specificity of SCOOP recognition by MIK2 and reveal an unprecedented mechanism by which N-glycosylation modification of LRR-RK promotes receptor activation.
History
DepositionFeb 8, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39093.png

Downloads & links

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Map

FileDownload / File: emd_39093.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 220 pix.
= 187. Å		0.85 Å/pix.
x 220 pix.
= 187. Å		0.85 Å/pix.
x 220 pix.
= 187. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.054888867 - 0.10850279
Average (Standard dev.)0.00024324056 (±0.0031585444)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 187.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39093_half_map_1.map
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Half map: #2

Fileemd_39093_half_map_2.map
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Sample components

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Entire : Ternary complex of MIK2-SCOOP12-BAK1

EntireName: Ternary complex of MIK2-SCOOP12-BAK1
Components
  • Complex: Ternary complex of MIK2-SCOOP12-BAK1
    • Protein or peptide: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
    • Protein or peptide: MDIS1-interacting receptor like kinase 2
    • Protein or peptide: Serine rich endogenous peptide 12
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of MIK2-SCOOP12-BAK1

SupramoleculeName: Ternary complex of MIK2-SCOOP12-BAK1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis (plant)

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Macromolecule #1: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

MacromoleculeName: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 19.160684 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
NAEGDALSAL KNSLADPNKV LQSWDATLVT PCTWFHVTCN SDNSVTRVDL GNANLSGQLV MQLGQLPNLQ YLELYSNNIT GTIPEQLGN LTELVSLDLY LNNLSGPIPS TLGRLKKLRF LRLNNNSLSG EIPRSLTAVL TLQVLDLSNN PLTGDIPVNG S FSLFTPIS FANTKLTPL

UniProtKB: BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

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Macromolecule #2: MDIS1-interacting receptor like kinase 2

MacromoleculeName: MDIS1-interacting receptor like kinase 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 71.858742 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: AVSATVEEAN ALLKWKSTFT NQTSSSKLSS WVNPNTSSFC TSWYGVACSL GSIIRLNLTN TGIEGTFEDF PFSSLPNLTF VDLSMNRFS GTISPLWGRF SKLEYFDLSI NQLVGEIPPE LGDLSNLDTL HLVENKLNGS IPSEIGRLTK VTEIAIYDNL L TGPIPSSF ...String:
AVSATVEEAN ALLKWKSTFT NQTSSSKLSS WVNPNTSSFC TSWYGVACSL GSIIRLNLTN TGIEGTFEDF PFSSLPNLTF VDLSMNRFS GTISPLWGRF SKLEYFDLSI NQLVGEIPPE LGDLSNLDTL HLVENKLNGS IPSEIGRLTK VTEIAIYDNL L TGPIPSSF GNLTKLVNLY LFINSLSGSI PSEIGNLPNL RELCLDRNNL TGKIPSSFGN LKNVTLLNMF ENQLSGEIPP EI GNMTALD TLSLHTNKLT GPIPSTLGNI KTLAVLHLYL NQLNGSIPPE LGEMESMIDL EISENKLTGP VPDSFGKLTA LEW LFLRDN QLSGPIPPGI ANSTELTVLQ LDTNNFTGFL PDTICRGGKL ENLTLDDNHF EGPVPKSLRD CKSLIRVRFK GNSF SGDIS EAFGVYPTLN FIDLSNNNFH GQLSANWEQS QKLVAFILSN NSITGAIPPE IWNMTQLSQL DLSSNRITGE LPESI SNIN RISKLQLNGN RLSGKIPSGI RLLTNLEYLD LSSNRFSSEI PPTLNNLPRL YYMNLSRNDL DQTIPEGLTK LSQLQM LDL SYNQLDGEIS SQFRSLQNLE RLDLSHNNLS GQIPPSFKDM LALTHVDVSH NNLQGPIPDN AAFRNAPPDA FEGNKDL CG SVNTTQGLKP CS

UniProtKB: MDIS1-interacting receptor like kinase 2

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Macromolecule #3: Serine rich endogenous peptide 12

MacromoleculeName: Serine rich endogenous peptide 12 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 1.318399 KDa
SequenceString:
PVRSSQSSQA GGR

UniProtKB: Serine rich endogenous peptide 12

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4mn8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 319127
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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