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- EMDB-34710: Cryo-EM structure of WeiTsing -

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Basic information

Entry
Database: EMDB / ID: EMD-34710
TitleCryo-EM structure of WeiTsing
Map data
Sample
  • Complex: WeiTsing
    • Protein or peptide: PRA1 family protein
KeywordsPentamer / Channel / MEMBRANE PROTEIN
Function / homology: / membrane / Transmembrane protein
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.14 Å
AuthorsQin L / Tang LH / Chen YH
Funding support China, 2 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2021YFA1300702 China
Chinese Academy of SciencesXDA24020305 China
CitationJournal: Cell / Year: 2023
Title: WeiTsing, a pericycle-expressed ion channel, safeguards the stele to confer clubroot resistance.
Authors: Wei Wang / Li Qin / Wenjing Zhang / Linghui Tang / Chao Zhang / Xiaojing Dong / Pei Miao / Meng Shen / Huilong Du / Hangyuan Cheng / Ke Wang / Xiangyun Zhang / Min Su / Hongwei Lu / Chang Li ...Authors: Wei Wang / Li Qin / Wenjing Zhang / Linghui Tang / Chao Zhang / Xiaojing Dong / Pei Miao / Meng Shen / Huilong Du / Hangyuan Cheng / Ke Wang / Xiangyun Zhang / Min Su / Hongwei Lu / Chang Li / Qiang Gao / Xiaojuan Zhang / Yun Huang / Chengzhi Liang / Jian-Min Zhou / Yu-Hang Chen /
Abstract: Plant roots encounter numerous pathogenic microbes that often cause devastating diseases. One such pathogen, Plasmodiophora brassicae (Pb), causes clubroot disease and severe yield losses on ...Plant roots encounter numerous pathogenic microbes that often cause devastating diseases. One such pathogen, Plasmodiophora brassicae (Pb), causes clubroot disease and severe yield losses on cruciferous crops worldwide. Here, we report the isolation and characterization of WeiTsing (WTS), a broad-spectrum clubroot resistance gene from Arabidopsis. WTS is transcriptionally activated in the pericycle upon Pb infection to prevent pathogen colonization in the stele. Brassica napus carrying the WTS transgene displayed strong resistance to Pb. WTS encodes a small protein localized in the endoplasmic reticulum (ER), and its expression in plants induces immune responses. The cryoelectron microscopy (cryo-EM) structure of WTS revealed a previously unknown pentameric architecture with a central pore. Electrophysiology analyses demonstrated that WTS is a calcium-permeable cation-selective channel. Structure-guided mutagenesis indicated that channel activity is strictly required for triggering defenses. The findings uncover an ion channel analogous to resistosomes that triggers immune signaling in the pericycle.
History
DepositionNov 9, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34710.png

Downloads & links

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Map

FileDownload / File: emd_34710.map.gz / Format: CCP4 / Size: 56.8 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 246 pix.
= 260.76 Å		1.06 Å/pix.
x 246 pix.
= 260.76 Å		1.06 Å/pix.
x 246 pix.
= 260.76 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.123
Minimum - Maximum-0.24685134 - 0.36910236
Average (Standard dev.)0.0007858322 (±0.013874205)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions246246246
Spacing246246246
CellA=B=C: 260.75998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34710_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #2

Fileemd_34710_half_map_2.map
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Sample components

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Entire : WeiTsing

EntireName: WeiTsing
Components
  • Complex: WeiTsing
    • Protein or peptide: PRA1 family protein

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Supramolecule #1: WeiTsing

SupramoleculeName: WeiTsing / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: PRA1 family protein

MacromoleculeName: PRA1 family protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 16.00399 KDa
Recombinant expressionOrganism: Schizosaccharomyces pombe (fission yeast)
SequenceString:
METVSAVNQT LPISGGEPVK FTTYSAAVHK VLVMVNAGIL GLLQLVSQQS SVLETHKAAF LCFCVFILFY AVLRVREAMD VRLQPGLVP RLIGHGSHLF GGLAALVLVS VVSTAFSIVL FLLWFIWLSA VVYLETNKPS ACPPQLPPV

UniProtKB: Transmembrane protein

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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

Concentration2.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 117360
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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