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- EMDB-30826: Cryo-EM structure of plant receptor like protein RXEG1 in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-30826
TitleCryo-EM structure of plant receptor like protein RXEG1 in complex with xyloglucanase XEG1 and BAK1
Map data
Sample
  • Complex: Ternary complex of XEG1 bounded RXEG1 with BAK1
    • Complex: xyloglucanase XEG1
      • Protein or peptide: Cell 12A endoglucanase
    • Complex: BAK1
      • Protein or peptide: Brassinosteroid insensitive 1-associated receptor kinase 1
    • Complex: RXEG1
      • Protein or peptide: Membrane-localized LRR receptor-like protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsLRR / PTI / Glycoside hydrolase / Inhibitor / PLANT PROTEIN
Function / homology
Function and homology information


response to other organism / cellulase activity / polysaccharide catabolic process / defense response / membrane
Similarity search - Function
: / Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Glycoside hydrolase family 11/12 / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat ...: / Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Glycoside hydrolase family 11/12 / Leucine-rich repeats, bacterial type / 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 / Leucine-rich repeat domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Membrane-localized LRR receptor-like protein / Cell 12A endoglucanase
Similarity search - Component
Biological speciesPhytophthora sojae (eukaryote) / Nicotiana benthamiana (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.92 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 China, Germany, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
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
DepositionDec 27, 2020-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_30826.png

Downloads & links

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Map

FileDownload / File: emd_30826.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.04857682 - 1.6493917
Average (Standard dev.)0.00126424 (±0.028881708)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
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_30826_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30826_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of XEG1 bounded RXEG1 with BAK1

EntireName: Ternary complex of XEG1 bounded RXEG1 with BAK1
Components
  • Complex: Ternary complex of XEG1 bounded RXEG1 with BAK1
    • Complex: xyloglucanase XEG1
      • Protein or peptide: Cell 12A endoglucanase
    • Complex: BAK1
      • Protein or peptide: Brassinosteroid insensitive 1-associated receptor kinase 1
    • Complex: RXEG1
      • Protein or peptide: Membrane-localized LRR receptor-like protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ternary complex of XEG1 bounded RXEG1 with BAK1

SupramoleculeName: Ternary complex of XEG1 bounded RXEG1 with BAK1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: xyloglucanase XEG1

SupramoleculeName: xyloglucanase XEG1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Phytophthora sojae (eukaryote)

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Supramolecule #3: BAK1

SupramoleculeName: BAK1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Nicotiana benthamiana (plant)

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Supramolecule #4: RXEG1

SupramoleculeName: RXEG1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Nicotiana benthamiana (plant)

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Macromolecule #1: Cell 12A endoglucanase

MacromoleculeName: Cell 12A endoglucanase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Phytophthora sojae (eukaryote)
Molecular weightTheoretical: 25.519551 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKGFFAGVVA AATLAVASAG DYCGQWDWAK STNYIVYNNL WNKNAAASGS QCTGVDKISG STIAWHTSYT WTGGAATEVK SYSNAALVF SKKQIKNIKS IPTKMKYSYS HSSGTFVADV SYDLFTSSTA SGSNEYEIMI WLAAYGGAGP ISSTGKAIAT V TIGSNSFK ...String:
MKGFFAGVVA AATLAVASAG DYCGQWDWAK STNYIVYNNL WNKNAAASGS QCTGVDKISG STIAWHTSYT WTGGAATEVK SYSNAALVF SKKQIKNIKS IPTKMKYSYS HSSGTFVADV SYDLFTSSTA SGSNEYEIMI WLAAYGGAGP ISSTGKAIAT V TIGSNSFK LYKGPNGSTT VFSFVATKTI TNFSADLQKF LSYLTKNQGL PSSQYLITLE AGTEPFVGTN AKMTVSSFSA AV N

UniProtKB: Cell 12A endoglucanase

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Macromolecule #2: Membrane-localized LRR receptor-like protein

MacromoleculeName: Membrane-localized LRR receptor-like protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 104.238852 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGKREYPSSA HFLVTLSLLL LQAAFGLTLC IEKERDALLE FKRGLSDNFG QLSTWGDEED KKECCKWKGI ECNKTTGHVI VLDLHNAFT CSASACFAPR LTGKLSPSLL ELEYLNFLDL SVNEFERSEI PRFICSFKRL EYLNLSSSFF SGLIPTQFKN L TSLRILDL ...String:
MGKREYPSSA HFLVTLSLLL LQAAFGLTLC IEKERDALLE FKRGLSDNFG QLSTWGDEED KKECCKWKGI ECNKTTGHVI VLDLHNAFT CSASACFAPR LTGKLSPSLL ELEYLNFLDL SVNEFERSEI PRFICSFKRL EYLNLSSSFF SGLIPTQFKN L TSLRILDL GYNNLIVKDL TWLSHLSSLE LLSLGGSDFQ VKNWFQEITK LPLLKELDLS LCGLSKLVPS PAEIANSSLI SL SVLHLCC NEFSSSAKYS WLFNFSTSLT SIDLSNNQLD GQIDDRFGNL MYLEHLNLAN ELNLKGGIPS SFGNLTRLRY LDM SNTRTY QWLPELFVRL SGSRKTLEVL GLNDNSMFGS LVDVTRFSAL KRLYLQKNVL NGFFMERFGQ VSSLEYLDLS DNQM RGPLP DLALFPSLRE LHLGSNHFNG RIPQGIGKLS QLKILDVSSN RLEGLPESMG QLSNLESFDA SYNVLKGTIT ESHLS NLSS LVDLDLSFNS LALKTSIDWL PPFQLQVINL PSCNLGPSFP KWLQSQNNYT VLDISLANIS DALPSWFSGL PPDIKI LNL SNNQISGRVS DLIENAYDYM VIDLSSNNFS GPLPLVPTNV QIFYLHKNQF FGSISSICKS TTGATSLDLS HNQFSGE LP DCWMNATNLA VLNLAYNNFS GKLPQSLGSL TNLEALYMRQ NSFSGMLPSL SQCQSLQILD LGGNKLTGRI PAWIGTDL L NLRILSLRFN KFYGSISPII CQLQFLQILD LSANGLAGKI PQCFNNFTLL HQENGLGEPM EFLVQGFYGK YPRHYSYLG NLLVQWKNQE AEYKNPLTYL KTIDLSSNKL VGGIPKEMAE MRGLKSLNLS RNDLNGSIIK GIGQMKMLES LDLSRNQLSG MIPKDLANL TFIGVLDLSN NHLSGRIPSS TQLQTFERSS YSGNAQLCGP PLQEC

UniProtKB: Membrane-localized LRR receptor-like protein

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Macromolecule #3: Brassinosteroid insensitive 1-associated receptor kinase 1

MacromoleculeName: Brassinosteroid insensitive 1-associated receptor kinase 1
type: protein_or_peptide / ID: 3 / 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 #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 13 / 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234633
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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