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- PDB-9uob: Plant-TaNNS -

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Basic information

Entry
Database: PDB / ID: 9uob
TitlePlant-TaNNS
Components
  • Protein kinase domain-containing protein
  • Somatic embryogenesis receptor kinase 1
  • TaNNS-C
KeywordsPLANT PROTEIN / Complex / Immunity
Function / homology
Function and homology information


somatic embryogenesis / regulation of defense response to fungus / brassinosteroid mediated signaling pathway / transmembrane receptor protein serine/threonine kinase activity / positive regulation of innate immune response / regulation of growth / post-embryonic development / non-specific serine/threonine protein kinase / protein serine/threonine kinase activity / ATP 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 / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain ...: / Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / 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. / 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
non-specific serine/threonine protein kinase / Protein kinase domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsWang, L. / Zhao, J. / Yin, C. / Chi, C. / Hou, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32472567 China
CitationJournal: Mol Plant / Year: 2025
Title: Recognition of a phytocytokine by the DEPR1-SERK2 receptor complex confers multi-pathogen resistance in wheat.
Authors: Lijun Wang / Jun Zhao / Chuanchun Yin / Hongxu Li / Yanan Xiao / Cuicui Du / Zhaoxi Lu / Yongjian Zhang / Fangshuai Jia / Jiaxin Hao / Jinghui Yan / Yi Zhang / Jian Li / Xinhua Ding / Zhifu ...Authors: Lijun Wang / Jun Zhao / Chuanchun Yin / Hongxu Li / Yanan Xiao / Cuicui Du / Zhaoxi Lu / Yongjian Zhang / Fangshuai Jia / Jiaxin Hao / Jinghui Yan / Yi Zhang / Jian Li / Xinhua Ding / Zhifu Han / Haitao Cui / Jijie Chai / Xingwang Deng / Cheng Chi / Shuguo Hou /
Abstract: The recognition of plant-derived immunogenic peptides, known as phytocytokines (PCKs), by cell surface receptors triggers immune signaling pathways that bolster basal plant defense against pathogens. ...The recognition of plant-derived immunogenic peptides, known as phytocytokines (PCKs), by cell surface receptors triggers immune signaling pathways that bolster basal plant defense against pathogens. However, little is known about the molecular mechanisms that underlie PCK-mediated immune regulation in wheat. In this study, we identified a wheat PCK, delta-like PCK (DEP), that robustly activates immune responses and confers multi-pathogen resistance. DEP is perceived by the leucine-rich repeat (LRR) receptor kinases (RKs) DEP RECEPTOR 1 (DEPR1) and SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 2 (SERK2) and triggers DEPR1- and SERK2-dependent immune signaling. Cryogenic electron microscopy structural analysis revealed that DEP2 binds to the extracellular LRR domain of DEPR1 and recruits SERK2 through a disulfide-bond-stabilized loop to promote DEPR1-SERK2 heterodimerization. Furthermore, we showed that the DEP2-DEPR1-SERK2 module confers wheat resistance to Xanthomonas translucens, Fusarium graminearum, and Fusarium pseudograminearum. We also demonstrated that this module enhances wheat resistance to X. translucens by antagonizing abscisic acid signaling. Collectively, our study reveals a novel PCK-mediated immune signaling pathway and suggests a promising strategy for engineering multi-pathogen resistance in wheat.
History
DepositionApr 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein kinase domain-containing protein
B: Somatic embryogenesis receptor kinase 1
C: TaNNS-C


Theoretical massNumber of molelcules
Total (without water)83,9443
Polymers83,9443
Non-polymers00
Water00
1


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

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Components

#1: Protein Protein kinase domain-containing protein / TaNNS-A


Mass: 61336.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: CFC21_042032 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A9R1FL93
#2: Protein Somatic embryogenesis receptor kinase 1 / TaNNS-B


Mass: 20076.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: SERK1, CFC21_017799 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A9R1E1Y6
#3: Protein/peptide TaNNS-C


Mass: 2530.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Gene: CFC21_011643 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A9R1IWD2
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: TaNNS / Type: COMPLEX
Details: The 3.3A resolution structure of wheat immune-related proteins.
Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Triticum aestivum (bread wheat)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

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

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57705 / Symmetry type: POINT
RefinementHighest resolution: 3.33 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026141
ELECTRON MICROSCOPYf_angle_d0.518365
ELECTRON MICROSCOPYf_dihedral_angle_d5.0821230
ELECTRON MICROSCOPYf_chiral_restr0.0451030
ELECTRON MICROSCOPYf_plane_restr0.0041074

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