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Yorodumi- EMDB-0683: Ligand-triggered allosteric ADP release primes a plant NLR complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0683 | |||||||||
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Title | Ligand-triggered allosteric ADP release primes a plant NLR complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ZAR1 / RKS1 / PLANT PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of defense response to bacterium / response to temperature stimulus / regulation of immune response / ADP binding / : / kinase activity / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity ...positive regulation of defense response to bacterium / response to temperature stimulus / regulation of immune response / ADP binding / : / kinase activity / defense response to Gram-negative bacterium / cell surface receptor signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / defense response to bacterium / phosphorylation / ATP binding / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis (plant) / Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Wang JZ / Wang J | |||||||||
Funding support | China, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0683.map.gz | 2.2 MB | EMDB map data format | |
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Header (meta data) | emd-0683-v30.xml emd-0683.xml | 14.2 KB 14.2 KB | Display Display | EMDB header |
Images | emd_0683.png | 48.8 KB | ||
Filedesc metadata | emd-0683.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0683 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0683 | HTTPS FTP |
-Related structure data
Related structure data | 6j5wMC 0681C 0682C 6j5uC 6j5vC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0683.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.091 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : ZAR1-RKS1 with ADP complex
Entire | Name: ZAR1-RKS1 with ADP complex |
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Components |
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-Supramolecule #1: ZAR1-RKS1 with ADP complex
Supramolecule | Name: ZAR1-RKS1 with ADP complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Arabidopsis (plant) |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: RKS1
Macromolecule | Name: RKS1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 40.142375 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: 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 UniProtKB: RKS1 |
-Macromolecule #2: Disease resistance RPP13-like protein 4
Macromolecule | Name: Disease resistance RPP13-like protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 97.163977 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: 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 UniProtKB: Disease resistance RPP13-like protein 4 |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 0.9 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 2092456 |
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Startup model | Type of model: OTHER |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 148718 |