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- EMDB-0688: Reconstitution and structure of a plant NLR resistosome conferrin... -

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Basic information

Entry
Database: EMDB / ID: EMD-0688
TitleReconstitution and structure of a plant NLR resistosome conferring immunity
Map data
Sample
  • Complex: resistosome
    • Protein or peptide: Probable serine/threonine-protein kinase PBL2
    • Protein or peptide: Protein kinase superfamily protein
    • Protein or peptide: Disease resistance RPP13-like protein 4
  • Ligand: URIDINE-5'-MONOPHOSPHATE
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
Function / homology
Function and homology information


positive regulation of defense response to bacterium / Tat protein binding / response to temperature stimulus / regulation of immune response / ADP binding / defense response / kinase activity / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase ...positive regulation of defense response to bacterium / Tat protein binding / response to temperature stimulus / regulation of immune response / ADP binding / defense response / kinase activity / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / defense response to bacterium / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane
Similarity search - Function
: / Receptor-like kinase WAK-like / 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 ...: / Receptor-like kinase WAK-like / 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 / 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. / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Probable serine/threonine-protein kinase PBL2 / Disease resistance RPP13-like protein 4 / Serine/threonine-protein kinase ZRK1
Similarity search - Component
Biological speciesArabidopsis (plant) / Arabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang JZ / Wang J / Hu MJ / Wang HW / Zhou JM / Chai JJ
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China31421001 China
National Natural Science Foundation of China31420103906 China
CitationJournal: Science / Year: 2019
Title: Reconstitution and structure of a plant NLR resistosome conferring immunity.
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.
History
DepositionJan 15, 2019-
Header (metadata) releaseMar 20, 2019-
Map releaseMar 20, 2019-
UpdateApr 12, 2023-
Current statusApr 12, 2023Processing site: PDBj / Status: Released

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Structure visualization

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-6j6i
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0688.png

Downloads & links

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Map

FileDownload / File: emd_0688.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.031787217 - 0.073630325
Average (Standard dev.)0.000100979334 (±0.0015970623)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 392.75998 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0320.0740.000

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Supplemental data

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Sample components

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Entire : resistosome

EntireName: resistosome
Components
  • Complex: resistosome
    • Protein or peptide: Probable serine/threonine-protein kinase PBL2
    • Protein or peptide: Protein kinase superfamily protein
    • Protein or peptide: Disease resistance RPP13-like protein 4
  • Ligand: URIDINE-5'-MONOPHOSPHATE
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Supramolecule #1: resistosome

SupramoleculeName: resistosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis (plant)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Probable serine/threonine-protein kinase PBL2

MacromoleculeName: Probable serine/threonine-protein kinase PBL2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 46.35643 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MGNCLDSSAK VDNSNHSPHA NSASSGSKVS SKTSRSTGPS GLSTTSYSTD SSFGPLPTLR TEGEILSSPN LKAFTFNELK NATKNFRQD NLLGEGGFGC VFKGWIDQTS LTASRPGSGI VVAVKQLKPE GFQGHKEWLT EVNYLGQLSH PNLVLLVGYC A EGENRLLV ...String:
MGNCLDSSAK VDNSNHSPHA NSASSGSKVS SKTSRSTGPS GLSTTSYSTD SSFGPLPTLR TEGEILSSPN LKAFTFNELK NATKNFRQD NLLGEGGFGC VFKGWIDQTS LTASRPGSGI VVAVKQLKPE GFQGHKEWLT EVNYLGQLSH PNLVLLVGYC A EGENRLLV YEFMPKGSLE NHLFRRGAQP LTWAIRMKVA VGAAKGLTFL HEAKSQVIYR DFKAANILLD ADFNAKLSDF GL AKAGPTG DNTHVSTKVI GTHGYAAPEY VATGRLTAKS DVYSFGVVLL ELISGRRAMD NSNGGNEYSL VDWATPYLGD KRK LFRIMD TKLGGQYPQK GAFTAANLAL QCLNPDAKLR PKMSEVLVTL EQLESVAKPG TKHTQMESPR FHHSSVMQKS PVRY SHDRP LLHMTPGASP LPSYTQSPRV R

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Macromolecule #2: Protein kinase superfamily protein

MacromoleculeName: Protein kinase superfamily protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 40.142375 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MKKQYLKSGS GTRKEKDKAK RWFLDNGSIF LRELVADCNG KSIPIRSFSP EQILKATNNF DSSCFVSQDV YYKWYRGEIE DRSYMIKRF SEDEITGKRH RVKEVYNDIV LSARMSNHSN FLQLLGCCLE FPFPVLVFEF AEHGAMNQRG GVIVNGEESL L PWSVRLKI ...String:
MKKQYLKSGS GTRKEKDKAK RWFLDNGSIF LRELVADCNG KSIPIRSFSP EQILKATNNF DSSCFVSQDV YYKWYRGEIE DRSYMIKRF SEDEITGKRH RVKEVYNDIV LSARMSNHSN FLQLLGCCLE FPFPVLVFEF AEHGAMNQRG GVIVNGEESL L PWSVRLKI GKEIANAVTY LHTAFPKIII HRDVKPMHVF LDKNWTAKLS DLSFSISLPE GKSRIEAEWV LGTFGYIDPL YH KTCFVTE YTDVYSFGIC LLVIITGKPA IMTISDGDLQ GILSLVRELC ENGKLDEVID PRLMKDITSG QRLQVEACVV LAL RCCKER DEDRPKMIQV AKELKQIEAS LKNSS

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Macromolecule #3: Disease resistance RPP13-like protein 4

MacromoleculeName: Disease resistance RPP13-like protein 4 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 97.163977 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MVDAVVTVFL EKTLNILEEK GRTVSDYRKQ LEDLQSELKY MQSFLKDAER QKRTNETLRT LVADLRELVY EAEDILVDCQ LADGDDGNE QRSSNAWLSR LHPARVPLQY KKSKRLQEIN ERITKIKSQV EPYFEFITPS NVGRDNGTDR WSSPVYDHTQ V VGLEGDKR ...String:
MVDAVVTVFL EKTLNILEEK GRTVSDYRKQ LEDLQSELKY MQSFLKDAER QKRTNETLRT LVADLRELVY EAEDILVDCQ LADGDDGNE QRSSNAWLSR LHPARVPLQY KKSKRLQEIN ERITKIKSQV EPYFEFITPS NVGRDNGTDR WSSPVYDHTQ V VGLEGDKR KIKEWLFRSN DSQLLIMAFV GMGGLGKTTI AQEVFNDKEI EHRFERRIWV SVSQTFTEEQ IMRSILRNLG DA SVGDDIG TLLRKIQQYL LGKRYLIVMD DVWDKNLSWW DKIYQGLPRG QGGSVIVTTR SESVAKRVQA RDDKTHRPEL LSP DNSWLL FCNVAFAAND GTCERPELED VGKEIVTKCK GLPLTIKAVG GLLLCKDHVY HEWRRIAEHF QDELRGNTSE TDNV MSSLQ LSYDELPSHL KSCILTLSLY PEDCVIPKQQ LVHGWIGEGF VMWRNGRSAT ESGEDCFSGL TNRCLIEVVD KTYSG TIIT CKIHDMVRDL VIDIAKKDSF SNPEGLNCRH LGISGNFDEK QIKVNHKLRG VVSTTKTGEV NKLNSDLAKK FTDCKY LRV LDISKSIFDA PLSEILDEIA SLQHLACLSL SNTHPLIQFP RSMEDLHNLQ ILDASYCQNL KQLQPCIVLF KKLLVLD MT NCGSLECFPK GIGSLVKLEV LLGFKPARSN NGCKLSEVKN LTNLRKLGLS LTRGDQIEEE ELDSLINLSK LMSISINC Y DSYGDDLITK IDALTPPHQL HELSLQFYPG KSSPSWLSPH KLPMLRYMSI CSGNLVKMQE PFWGNENTHW RIEGLMLSS LSDLDMDWEV LQQSMPYLRT VTANWCPELE SFAIEDVGFR GGVWMKTPLH RT

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Macromolecule #4: URIDINE-5'-MONOPHOSPHATE

MacromoleculeName: URIDINE-5'-MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: U5P
Molecular weightTheoretical: 324.181 Da
Chemical component information

ChemComp-U:
URIDINE-5'-MONOPHOSPHATE

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Macromolecule #5: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 5 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
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: 0.01 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.7000000000000001 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

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Image processing

Particle selectionNumber selected: 2092456
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Number images used: 376858
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

3tl8

RefinementSpace: REAL
Output model

PDB-6j6i:
Reconstitution and structure of a plant NLR resistosome conferring immunity

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