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- EMDB-45438: Dodecameric state of the NRC4 resistosome -

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Basic information

Entry
Database: EMDB / ID: EMD-45438
TitleDodecameric state of the NRC4 resistosome
Map data
Sample
  • Complex: Dodecameric state of the NRC4 resistosome
    • Protein or peptide: NLR-required for cell death 4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsplant resistosome / PLANT PROTEIN
Function / homology
Function and homology information


response to other organism / ADP binding / defense response
Similarity search - Function
Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NLR-required for cell death 4
Similarity search - Component
Biological speciesNicotiana benthamiana (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsLiu F / Yang Z / Nogales E / Staskawicz BJ
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell / Year: 2024
Title: Activation of the helper NRC4 immune receptor forms a hexameric resistosome.
Authors: Furong Liu / Zhenlin Yang / Chao Wang / Zhang You / Raoul Martin / Wenjie Qiao / Jian Huang / Pierre Jacob / Jeffery L Dangl / Jan E Carette / Sheng Luan / Eva Nogales / Brian J Staskawicz /
Abstract: Innate immune responses to microbial pathogens are regulated by intracellular receptors known as nucleotide-binding leucine-rich repeat receptors (NLRs) in both the plant and animal kingdoms. Across ...Innate immune responses to microbial pathogens are regulated by intracellular receptors known as nucleotide-binding leucine-rich repeat receptors (NLRs) in both the plant and animal kingdoms. Across plant innate immune systems, "helper" NLRs (hNLRs) work in coordination with "sensor" NLRs (sNLRs) to modulate disease resistance signaling pathways. Activation mechanisms of hNLRs based on structures are unknown. Our research reveals that the hNLR, known as NLR required for cell death 4 (NRC4), assembles into a hexameric resistosome upon activation by the sNLR Bs2 and the pathogenic effector AvrBs2. This conformational change triggers immune responses by facilitating the influx of calcium ions (Ca) into the cytosol. The activation mimic alleles of NRC2, NRC3, or NRC4 alone did not induce Ca influx and cell death in animal cells, suggesting that unknown plant-specific factors regulate NRCs' activation in plants. These findings significantly advance our understanding of the regulatory mechanisms governing plant immune responses.
History
DepositionJun 21, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 18, 2024-
Current statusSep 18, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45438.png

Downloads & links

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Map

FileDownload / File: emd_45438.map.gz / Format: CCP4 / Size: 280.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 419 pix.
= 419. Å		1 Å/pix.
x 419 pix.
= 419. Å		1 Å/pix.
x 419 pix.
= 419. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.544
Minimum - Maximum-0.10624351 - 14.98939
Average (Standard dev.)0.026849914 (±0.54269016)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions419419419
Spacing419419419
CellA=B=C: 419.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Dodecameric state of the NRC4 resistosome

EntireName: Dodecameric state of the NRC4 resistosome
Components
  • Complex: Dodecameric state of the NRC4 resistosome
    • Protein or peptide: NLR-required for cell death 4
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Dodecameric state of the NRC4 resistosome

SupramoleculeName: Dodecameric state of the NRC4 resistosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Nicotiana benthamiana (plant)

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Macromolecule #1: NLR-required for cell death 4

MacromoleculeName: NLR-required for cell death 4 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 100.074695 KDa
SequenceString: MADAVVNFEV ENLLQLLTDN VKLIGSAKGE LENLLKEVQH LKGFLDDAAK LPSDSEQWKV LVEEIQKTVH TAEDAVDKFV VQAKLHKEK NKMARILDVG HLATVRNLAA EVKGIHDQVK ELRLNNQALQ ARPTLELPKK GSSETTQQGP ALEDDEVVGF D EEANKVIN ...String:
MADAVVNFEV ENLLQLLTDN VKLIGSAKGE LENLLKEVQH LKGFLDDAAK LPSDSEQWKV LVEEIQKTVH TAEDAVDKFV VQAKLHKEK NKMARILDVG HLATVRNLAA EVKGIHDQVK ELRLNNQALQ ARPTLELPKK GSSETTQQGP ALEDDEVVGF D EEANKVIN RLVKESKDLD IIPVVGMPGL GKTTLARKIY KDPKLSYEFF GVHWVYVGQS YKIKDVFLNI LKFFTRRTED YQ HEDVDAL AKVIAGFINK GGRCLICLDD VWETKVIDYV KTIFPENEKG HRVMMTTRNK VLATYANSDP HDLKFLTPKE SFE LLVKRV FGKKPCPKDL VGHGESIAGK CGGVPLAVVV IAGALRGRPN TSDWIRVERN VVQHLYTNSE ESCLKFVEMS YDHL PQEVQ TCFLYCGVFP RGFDIPSWKV IRLWIAEGLI KPQESYTLEE IAEFYLNDLV NRNLVILQQK RSDGQIKTCR LHVML HQFC KKEASNKWLF QEVSLTPDQA IPIEDPNKSR RLCIQPSNLK DFLSKKPSAE HVRSFYCFSS KEKQIRGLTP NDIKLI HKA FPLVRVLDVE SLKFLFSKDF NQLFHLRYIA ISGDFNAIPL TFGKFWNLQT LILNTSTSES TLDVKADIWN MLQLRHL HT NIPAKLQPPT ATTSGKASCL QTLCMVAPES CEKEVLAKAC HLKKLSIRGQ MAAFLGAYKG GINNLVELKC LEQLKLLN D VLYMNKAPHL PQTFSQLVRT VKKLTLTNTR FAWSEADKLG QLESLEILKF KENAFAGDSW KPKMGFSALR VLWIERAEF ETWEASEINF PVLRNLVLMS CDKLETVPFE LANLSDLYEM RLENTSKAVK SAKAILESKT DKNIKFNLTI FPPEAGSKAT Q

UniProtKB: NLR-required for cell death 4

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28066
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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