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- EMDB-0681: Ligand-triggered allosteric ADP release primes a plant NLR complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0681
TitleLigand-triggered allosteric ADP release primes a plant NLR complex
Map data
Sample
  • Complex: ZAR1-RKS1 with ADP complex
    • Protein or peptide: Disease resistance RPP13-like protein 4
  • Protein or peptide: Probable serine/threonine-protein kinase PBL2
  • Protein or peptide: Protein kinase superfamily protein
  • Ligand: URIDINE-5'-MONOPHOSPHATE
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: 3.9 Å
AuthorsWang JZ / Wang J / Meijuan H / 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: Ligand-triggered allosteric ADP release primes a plant NLR complex.
Authors: Jizong Wang / Jia Wang / Meijuan Hu / Shan Wu / Jinfeng Qi / Guoxun Wang / Zhifu Han / Yijun Qi / Ning Gao / Hong-Wei Wang / Jian-Min Zhou / Jijie Chai /
Abstract: Pathogen recognition by nucleotide-binding (NB), leucine-rich repeat (LRR) receptors (NLRs) plays roles in plant immunity. The pv. effector AvrAC uridylylates the PBL2 kinase, and the latter (PBL2) ...Pathogen recognition by nucleotide-binding (NB), leucine-rich repeat (LRR) receptors (NLRs) plays roles in plant immunity. The pv. effector AvrAC uridylylates the PBL2 kinase, and the latter (PBL2) acts as a ligand to activate the NLR ZAR1 precomplexed with the RKS1 pseudokinase. Here we report the cryo-electron microscopy structures of ZAR1-RKS1 and ZAR1-RKS1-PBL2 in an inactive and intermediate state, respectively. The ZAR1 domain, compared with animal NLR domains, is differently positioned to sequester ZAR1 in an inactive state. Recognition of PBL2 is exclusively through RKS1, which interacts with ZAR1 PBL2 binding stabilizes the RKS1 activation segment, which sterically blocks ZAR1 adenosine diphosphate (ADP) binding. This engenders a more flexible NB domain without conformational changes in the other ZAR1 domains. Our study provides a structural template for understanding plant NLRs.
History
DepositionJan 12, 2019-
Header (metadata) releaseApr 3, 2019-
Map releaseApr 3, 2019-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6j5u
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0681.png

Downloads & links

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Map

FileDownload / File: emd_0681.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 160 pix.
= 174.56 Å		1.09 Å/pix.
x 160 pix.
= 174.56 Å		1.09 Å/pix.
x 160 pix.
= 174.56 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: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.10283787 - 0.19056778
Average (Standard dev.)0.00069471967 (±0.006741516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 174.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z174.560174.560174.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1030.1910.001

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Supplemental data

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Sample components

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Entire : ZAR1-RKS1 with ADP complex

EntireName: ZAR1-RKS1 with ADP complex
Components
  • Complex: ZAR1-RKS1 with ADP complex
    • Protein or peptide: Disease resistance RPP13-like protein 4
  • Protein or peptide: Probable serine/threonine-protein kinase PBL2
  • Protein or peptide: Protein kinase superfamily protein
  • Ligand: URIDINE-5'-MONOPHOSPHATE

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Supramolecule #1: ZAR1-RKS1 with ADP complex

SupramoleculeName: ZAR1-RKS1 with ADP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis (plant)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Disease resistance RPP13-like protein 4

MacromoleculeName: Disease resistance RPP13-like protein 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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 #2: Probable serine/threonine-protein kinase PBL2

MacromoleculeName: Probable serine/threonine-protein kinase PBL2 / type: protein_or_peptide / ID: 2 / 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 #3: Protein kinase superfamily protein

MacromoleculeName: Protein kinase superfamily protein / type: protein_or_peptide / ID: 3 / 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 #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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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: 3342829
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Number images used: 404311
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-6j5u:
Ligand-triggered allosteric ADP release primes a plant NLR complex

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