[English] 日本語
Yorodumi
- EMDB-51910: Cryo-EM structure of an octameric G10-resistosome from wheat in '... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51910
TitleCryo-EM structure of an octameric G10-resistosome from wheat in 'back-to-back' arrangement
Map datathis is the final post-processed map
Sample
  • Complex: Wai-3 resistosome as double octamer in back-to-back arrangement
    • Protein or peptide: NB-ARC domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsResistance / G10-NLR / Wheat / resistosome / PLANT PROTEIN
Function / homology
Function and homology information


defense response / ADP binding
Similarity search - Function
: / Plant disease resistance protein RPS2-like, leucine-rich repeats / Disease resistance protein Winged helix domain / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. ...: / Plant disease resistance protein RPS2-like, leucine-rich repeats / Disease resistance protein Winged helix domain / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NB-ARC domain-containing protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGuo GH / Zhao H / Lukoyanova N / Selvaraj M / Jones J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Gatsby Charitable Foundation United Kingdom
CitationJournal: Biorxiv / Year: 2025
Title: An activated wheat CCG10-NLR immune receptor forms an octameric resistosome
Authors: Guo G / Zhao H / Bai K / Wu Q / Dong L / Lu L / Chen Y / Hou Y / Lu J / Lu P / Li M / Zhang H / Wang G / Zhu K / Huang B / Cui X / Fu H / Hu C / Chu Z / Lyu X / Kamoun S / Wang C / Liu Z / Selvaraj M / Jones JDG
History
DepositionOct 25, 2024-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51910.png

Downloads & links

-
Map

FileDownload / File: emd_51910.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationthis is the final post-processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.04183984 - 0.07703998
Average (Standard dev.)0.00030827973 (±0.0024932043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51910_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: This is half map 1 flipped to match primary map

Fileemd_51910_half_map_1.map
AnnotationThis is half map 1 flipped to match primary map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: This is half map 2 flipped to match primary map

Fileemd_51910_half_map_2.map
AnnotationThis is half map 2 flipped to match primary map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Wai-3 resistosome as double octamer in back-to-back arrangement

EntireName: Wai-3 resistosome as double octamer in back-to-back arrangement
Components
  • Complex: Wai-3 resistosome as double octamer in back-to-back arrangement
    • Protein or peptide: NB-ARC domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Wai-3 resistosome as double octamer in back-to-back arrangement

SupramoleculeName: Wai-3 resistosome as double octamer in back-to-back arrangement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: This is an assembly of Wai-3 resistance protein containing 16 chains, in D8 symmetry in a back-to-back arrangement of two octamer
Source (natural)Organism: Triticum aestivum (bread wheat)
Molecular weightTheoretical: 1.7 MDa

-
Macromolecule #1: NB-ARC domain-containing protein

MacromoleculeName: NB-ARC domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Triticum aestivum (bread wheat) / Strain: M3405
Molecular weightTheoretical: 107.700422 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MADAISAAGS CEQPECECLD GTGMLDAAAR EVASFLHLKS NWSDLDKAKK LLLAVETTVR ARVTAEVDKL NICDPQVQVW LRRVEELQL DAIDEDYSQL RKYSCLGQCT IHAHRRASIG RRVLEALDEA NKLIEEGRRF KKFGFKPLPK IVDPLPQIKT F GLETMLSQ ...String:
MADAISAAGS CEQPECECLD GTGMLDAAAR EVASFLHLKS NWSDLDKAKK LLLAVETTVR ARVTAEVDKL NICDPQVQVW LRRVEELQL DAIDEDYSQL RKYSCLGQCT IHAHRRASIG RRVLEALDEA NKLIEEGRRF KKFGFKPLPK IVDPLPQIKT F GLETMLSQ LYDLFEKGDS NIIGVWGQGG VGKTTLLHVF NNDLEKKAHD YQVVIFIEVS NSEALNTVEI QQTISERLNL PW NDAEPIA KRARFLIKAL GRKRFVILLD DVRKKFCLED VGIPTPDINS QSKLILTSRY REVCFQMNAQ RSLIEMQILG NDA SWELFL SKLSTETSAA VEPLGSQSAT REHAMKIAQS CGGLPLALNV IGTAVAGLEE GEWQSAADAI ATNMDNIDGV DEMF GRLKY SFDRLTPTQQ QCFLYCTLFP EYGSISKEQL IGYWLAEGLL LNDSEKGYQI IRSLVSACLL QVSGSMSSKV KMHHV IRQL GLWLVNKSDT KFLVQPGMAL DNAPSAEEWN EATRISIMSN NITELSFSPK CKNVTTLLMQ NNPNLNKMSY GFFRTM SSL KVLDLSHTAI TSLPECDALV ALEHLNLSHT HIMRLPERLW LLKELRHLDL SVTVAFEDTM NNCSKLHKLK VLNLFRS HY GIRDVDNLNL DSLKELLFLG ITIYAEDVLK KLNMPRPLAK STHRLNLKYC AEMQSIKISD LSHMEHLEEL YVESCYDL N TVVADAELTT SQLQFLTLSV LPSLESVLVA PMSHNFQYIR KLIISHCPKL SNITWVRRLQ LLERLVISHC DGVLEIVED EEQYGEQMKM QDHASYEQEE HAMVETSRND TGQSDFPKLR LIVLTGLKKL RSICKAREFP CLETLRVEDC PNLRSIPLSC THNYWKLKQ ICGSVEWWEK LQWENRKEVA CLDSKYFIPI GSDYKDHDGD YKDHDLDAAA ADYKDDDDK

UniProtKB: NB-ARC domain-containing protein

-
Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 16 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.3 mg/mL
BufferpH: 7.5 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: sodium chloride
Details: 150mM NaCl 150mM Tris (pH 7.5) 1mM MgCl2 1mM EDTA 10% glycerol 0.2% NP40
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis is a wheat resistosome protein purified from Nicotiana benthamiana

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV / Details: Detector post GIF
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7000 / Average exposure time: 1.94 sec. / Average electron dose: 50.0 e/Å2
Details: 7000 micrographs collected as movies. 5 images per hole. (Fast data 660 images per hour)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio starting model in Relion
Final reconstructionApplied symmetry - Point group: D8 (2x8 fold dihedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 27667
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0)
Final 3D classificationNumber classes: 4 / Software - Name: RELION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 137
Output model

PDB-9h73:
Cryo-EM structure of an octameric G10-resistosome from wheat in 'back-to-back' arrangement

+
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