[English] 日本語
Yorodumi
- EMDB-64376: Plant-TaNNS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64376
TitlePlant-TaNNS
Map data
Sample
  • Complex: TaNNS
    • Protein or peptide: Protein kinase domain-containing protein
    • Protein or peptide: Somatic embryogenesis receptor kinase 1
    • Protein or peptide: TaNNS-C
KeywordsComplex / Immunity / PLANT PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsWang L / Zhao J / Yin C / Chi C / Hou S
Funding support China, 1 items
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, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_64376.png

Downloads & links

-
Map

FileDownload / File: emd_64376.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.194
Minimum - Maximum-0.84597236 - 1.4576644
Average (Standard dev.)-0.00007066493 (±0.034269303)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_64376_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_64376_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : TaNNS

EntireName: TaNNS
Components
  • Complex: TaNNS
    • Protein or peptide: Protein kinase domain-containing protein
    • Protein or peptide: Somatic embryogenesis receptor kinase 1
    • Protein or peptide: TaNNS-C

-
Supramolecule #1: TaNNS

SupramoleculeName: TaNNS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The 3.3A resolution structure of wheat immune-related proteins.
Source (natural)Organism: Triticum aestivum (bread wheat)

-
Macromolecule #1: Protein kinase domain-containing protein

MacromoleculeName: Protein kinase domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 61.336746 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: QAADDRQLLI RIKRVWRDPP VLAAWNGSGD HCTWPYVTCD ASGRVTSLSL ANTGVAGPFP DAIGGLSGLT SLDLSGNYLD GELPADIGR ALGKNLTSLM LNGNYFNGTI PTSLSRLKNL QSLALDNNFL AGTIPAELGD LTGLQMLTLA NNSFSVGVLP A SFKNLTQL ...String:
QAADDRQLLI RIKRVWRDPP VLAAWNGSGD HCTWPYVTCD ASGRVTSLSL ANTGVAGPFP DAIGGLSGLT SLDLSGNYLD GELPADIGR ALGKNLTSLM LNGNYFNGTI PTSLSRLKNL QSLALDNNFL AGTIPAELGD LTGLQMLTLA NNSFSVGVLP A SFKNLTQL KTFWAAICNL TGDFPSYVAE MRELEVLDLS VNALTGSIPP AIWNLAKLQT MALFANNFTG GVVVADGAFS AV NLVMIDL SSNHRLSGPI PEAFGHLPNL ETLNLYFNNF SGEIPASIGR LPSLVTLSLF RNRLTGRLPP DLGKNSSAGL MYI DVDDNE ISGAIPEGLC ANGKFQSLIA RNNRLNGSIP AGLASCATLN NLMLGNNQLS GEVPEALWTV PQLEYVLLRN NRLS GSLPV KMFINLSTLH IENNQFGGNI PAAAVGLREF IAGNNNFSGE MPASLGKGMP LLQAMNLSGN QLFGGIPSSV AKLRL LTQL DLSRNQLAGE IPAELGAMRV LSALDLSSNK LSGYIPPPLA GLPLTFLNLS SNQLDGQVPA GLATAAYDRS FLGNPG LCH AGLGPRYLTG VRSCAAGS

UniProtKB: Protein kinase domain-containing protein

-
Macromolecule #2: Somatic embryogenesis receptor kinase 1

MacromoleculeName: Somatic embryogenesis receptor kinase 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 20.076572 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
NTEGDALYSL RQSLKDANNV LQSWDPTLVN PCTWFHVTCN TDNSVIRVDL GNAQLSGALV SQLGQLKNLQ YLELYSNNIS GTIPLELGN LTNLVSLDLY LNKFTGGIPD TLGKLLKLRF LRLNNNSLSG QIPQSLTNIS TLQVLDLSNN NLSGAVPSTG S FSLFTPIS FGNNPNLCGP GTTKPCPGA

UniProtKB: non-specific serine/threonine protein kinase

-
Macromolecule #3: TaNNS-C

MacromoleculeName: TaNNS-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 2.530781 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
PRGGGSAGAP NGCTNNPKHP PGGKCHG

UniProtKB: Uncharacterized protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57705
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more