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- EMDB-0680: Reconstitution and structure of a plant NLR resistosome conferrin... -

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Basic information

Entry
Database: EMDB / Id: 680
TitleReconstitution and structure of a plant NLR resistosome conferring immunity
Map data
Sampleresistosome
  • Probable serine/threonine-protein kinase PBL2
  • Protein kinase superfamily protein
  • Disease resistance RPP13-like protein 4
  • (ligand) x 3
Func homologyProtein kinase-like domain superfamily / Protein kinase domain / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Protein kinase, ATP binding site / NB-ARC domain / Serine/threonine-protein kinase, active site / NB-ARC / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine kinase ...Protein kinase-like domain superfamily / Protein kinase domain / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Protein kinase, ATP binding site / NB-ARC domain / Serine/threonine-protein kinase, active site / NB-ARC / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine kinase / Protein kinase domain / Protein kinases ATP-binding region signature. / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile. / Virus X resistance protein-like, coiled-coil domain / Tat protein binding / ADP binding / defense response / protein self-association / non-specific serine/threonine protein kinase / defense response to Gram-negative bacterium / protein serine/threonine kinase activity / ATP binding / plasma membrane / nucleus / Probable serine/threonine-protein kinase PBL2 / Disease resistance RPP13-like protein 4 / Protein kinase superfamily protein
Function and homology information
SourceArabidopsis (plant) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang JZ / Wang J / Hu MJ / Wang HW / Zhou JM / Chai JJ
CitationJournal: Science / Year: 2019
Title: Reconstitution and structure of a plant NLR resistosome conferring immunity.
P-authors: Jizong Wang / Meijuan Hu / Jia Wang / Jinfeng Qi / Zhifu Han / Guoxun Wang / Yijun Qi / Hong-Wei Wang / Jian-Min Zhou / Jijie Chai /
Abstract: Nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen effectors to trigger plant immunity. Biochemical mechanisms underlying plant NLR activation have until now remained poorly ...Nucleotide-binding, leucine-rich repeat receptors (NLRs) perceive pathogen effectors to trigger plant immunity. Biochemical mechanisms underlying plant NLR activation have until now remained poorly understood. We reconstituted an active complex containing the coiled-coil NLR ZAR1, the pseudokinase RKS1, uridylated protein kinase PBL2, and 2'-deoxyadenosine 5'-triphosphate (dATP), demonstrating the oligomerization of the complex during immune activation. The cryo-electron microscopy structure reveals a wheel-like pentameric ZAR1 resistosome. Besides the nucleotide-binding domain, the coiled-coil domain of ZAR1 also contributes to resistosome pentamerization by forming an α-helical barrel that interacts with the leucine-rich repeat and winged-helix domains. Structural remodeling and fold switching during activation release the very N-terminal amphipathic α helix of ZAR1 to form a funnel-shaped structure that is required for the plasma membrane association, cell death triggering, and disease resistance, offering clues to the biochemical function of a plant resistosome.
Validation ReportPDB-ID: 6j5t

SummaryFull reportAbout validation report
DateDeposition: Jan 12, 2019 / Header (metadata) release: Mar 20, 2019 / Map release: Mar 20, 2019 / Last update: Apr 17, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6j5t
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_0680.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.09 Å/pix.
= 392.76 Å
360 pix
1.09 Å/pix.
= 392.76 Å
360 pix
1.09 Å/pix.
= 392.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density
Contour Level:0.013 (by author), 0.013 (movie #1):
Minimum - Maximum-0.025375234 - 0.09131176
Average (Standard dev.)0.0002763708 (0.0027265695)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 392.75998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z392.760392.760392.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0250.0910.000

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Supplemental data

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Sample components

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Entire resistosome

EntireName: resistosome / Number of components: 7

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Component #1: protein, resistosome

ProteinName: resistosome / Recombinant expression: No
MassExperimental: 130 kDa
SourceSpecies: Arabidopsis (plant)
Source (engineered)Expression System: Insect cell expression vector pTIE1 (others)

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Component #2: protein, Probable serine/threonine-protein kinase PBL2

ProteinName: Probable serine/threonine-protein kinase PBL2 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 46.35643 kDa
SourceSpecies: Arabidopsis thaliana (thale cress)
Source (engineered)Expression System: Insect cell expression vector pTIE1 (others)

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Component #3: protein, Protein kinase superfamily protein

ProteinName: Protein kinase superfamily protein / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 40.142375 kDa
SourceSpecies: Arabidopsis thaliana (thale cress)
Source (engineered)Expression System: Insect cell expression vector pTIE1 (others)

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Component #4: protein, Disease resistance RPP13-like protein 4

ProteinName: Disease resistance RPP13-like protein 4 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 97.163977 kDa
SourceSpecies: Arabidopsis thaliana (thale cress)
Source (engineered)Expression System: Insect cell expression vector pTIE1 (others)

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Component #5: ligand, [(2~{S})-2-azanyl-3-oxidanylidene-propyl] [(2~{R},3~{S},4...

LigandName: [(2~{S})-2-azanyl-3-oxidanylidene-propyl] [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.395259 kDa

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Component #6: ligand, [(2~{R},3~{S})-3-azanyl-4-oxidanylidene-butan-2-yl] [(2~{...

LigandName: [(2~{R},3~{S})-3-azanyl-4-oxidanylidene-butan-2-yl] [(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.409286 kDa

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Component #7: ligand, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

LigandName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 0.491182 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionPh: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal) / Cs: 0.01 mm / Imaging mode: BRIGHT FIELD / Defocus: 700.0 - 900.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C5 (5 fold cyclic) / Number of projections: 196707
3D reconstructionSoftware: RELION / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement space: REAL
Input PDB model: 3TL8
Output model

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