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- EMDB-32293: Cryo-EM structure of plant receptor like kinase NbBAK1 in RXEG1-B... -

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Basic information

Entry
Database: EMDB / ID: EMD-32293
TitleCryo-EM structure of plant receptor like kinase NbBAK1 in RXEG1-BAK1-XEG1 complex
Map data
Sample
  • Complex: BAK1
    • Protein or peptide: Brassinosteroid insensitive 1-associated receptor kinase 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLRR / PTI / Glycoside hydrolase / Inhibitor / PLANT PROTEIN
Biological speciesNicotiana benthamiana (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsSun Y / Wang Y / Zhang XX / Chen ZD / Xia YQ / Sun YJ / Zhang MM / Xiao Y / Han ZF / Wang YC / Chai JJ
Funding support Germany, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) Germany
Alexander von Humboldt Foundation Germany
CitationJournal: Nature / Year: 2022
Title: Plant receptor-like protein activation by a microbial glycoside hydrolase.
Authors: Yue Sun / Yan Wang / Xiaoxiao Zhang / Zhaodan Chen / Yeqiang Xia / Lei Wang / Yujing Sun / Mingmei Zhang / Yu Xiao / Zhifu Han / Yuanchao Wang / Jijie Chai /
Abstract: Plants rely on cell-surface-localized pattern recognition receptors to detect pathogen- or host-derived danger signals and trigger an immune response. Receptor-like proteins (RLPs) with a leucine- ...Plants rely on cell-surface-localized pattern recognition receptors to detect pathogen- or host-derived danger signals and trigger an immune response. Receptor-like proteins (RLPs) with a leucine-rich repeat (LRR) ectodomain constitute a subgroup of pattern recognition receptors and play a critical role in plant immunity. Mechanisms underlying ligand recognition and activation of LRR-RLPs remain elusive. Here we report a crystal structure of the LRR-RLP RXEG1 from Nicotiana benthamiana that recognizes XEG1 xyloglucanase from the pathogen Phytophthora sojae. The structure reveals that specific XEG1 recognition is predominantly mediated by an amino-terminal and a carboxy-terminal loop-out region (RXEG1(ID)) of RXEG1. The two loops bind to the active-site groove of XEG1, inhibiting its enzymatic activity and suppressing Phytophthora infection of N. benthamiana. Binding of XEG1 promotes association of RXEG1(LRR) with the LRR-type co-receptor BAK1 through RXEG1(ID) and the last four conserved LRRs to trigger RXEG1-mediated immune responses. Comparison of the structures of apo-RXEG1(LRR), XEG1-RXEG1(LRR) and XEG1-BAK1-RXEG1(LRR) shows that binding of XEG1 induces conformational changes in the N-terminal region of RXEG1(ID) and enhances structural flexibility of the BAK1-associating regions of RXEG1(LRR). These changes allow fold switching of RXEG1(ID) for recruitment of BAK1(LRR). Our data reveal a conserved mechanism of ligand-induced heterodimerization of an LRR-RLP with BAK1 and suggest a dual function for the LRR-RLP in plant immunity.
History
DepositionNov 26, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32293.png

Downloads & links

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Map

FileDownload / File: emd_32293.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.64 Å		1.06 Å/pix.
x 240 pix.
= 254.64 Å		1.06 Å/pix.
x 240 pix.
= 254.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.038746122 - 1.7915784
Average (Standard dev.)0.000089012785 (±0.011777954)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_32293_half_map_1.map
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Half map: #2

Fileemd_32293_half_map_2.map
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Sample components

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Entire : BAK1

EntireName: BAK1
Components
  • Complex: BAK1
    • Protein or peptide: Brassinosteroid insensitive 1-associated receptor kinase 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: BAK1

SupramoleculeName: BAK1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nicotiana benthamiana (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
Source (natural)Organism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 24.514012 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDQWILGILG FVSTFLCLIG LLLVPVSANI EGDALNALKT NLADPNNVLQ SWDPTLVNPC TWFHVTCNSE NSVTRVDLGN ANLSGQLVP QLGQLPNLQY LELYSNNISG RIPFELGNLT NLVSLDLYLN RLNGPIPDTL GKLQKLRFLR LNNNSLNGRI P MLLTTVIS ...String:
MDQWILGILG FVSTFLCLIG LLLVPVSANI EGDALNALKT NLADPNNVLQ SWDPTLVNPC TWFHVTCNSE NSVTRVDLGN ANLSGQLVP QLGQLPNLQY LELYSNNISG RIPFELGNLT NLVSLDLYLN RLNGPIPDTL GKLQKLRFLR LNNNSLNGRI P MLLTTVIS LQVLDLSNNN LTGPVPVNGS FSLFTPISFA NNPLDIPPAA PPPPISPMPP SSSGVGNSAT

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36117
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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